Loading doc/src/Build_extras.rst +1 −1 Original line number Diff line number Diff line Loading @@ -177,7 +177,7 @@ KIM package To build with this package, the KIM library with API v2 must be downloaded and built on your system. It must include the KIM models that you want to use with LAMMPS. If you want to use the :doc:`kim\_query <kim_commands>` use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>` command, you also need to have libcurl installed with the matching development headers and the curl-config tool. Loading doc/src/Build_settings.rst +6 −6 Original line number Diff line number Diff line Loading @@ -5,11 +5,11 @@ LAMMPS can be built with several optional settings. Each sub-section explain how to do this for building both with CMake and make. | :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS | :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command | :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command | :ref:`Size of LAMMPS data types <size>` | :ref:`Read or write compressed files <gzip>` | :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command | :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command | :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command | :ref:`Memory allocation alignment <align>` | :ref:`Workaround for long long integers <longlong>` | :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library Loading Loading @@ -66,7 +66,7 @@ FFT library --------------------- When the KSPACE package is included in a LAMMPS build, the :doc:`kspace\_style pppm <kspace_style>` command performs 3d FFTs which :doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which require use of an FFT library to compute 1d FFTs. The KISS FFT library is included with LAMMPS but other libraries can be faster. LAMMPS can use them if they are available on your system. Loading Loading @@ -134,7 +134,7 @@ However, note that long-range Coulombics are only a portion of the per-timestep CPU cost, FFTs are only a portion of long-range Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel communication can be costly). A breakdown of these timings is printed to the screen at the end of a run using the :doc:`kspace\_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>` to the screen at the end of a run using the :doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>` doc page gives more details. FFTW is a fast, portable FFT library that should also work on any Loading Loading @@ -235,7 +235,7 @@ support 8-byte integers. It allows for: Atom IDs are not required for atomic systems which do not store bond topology information, though IDs are enabled by default. The :doc:`atom\_modify id no <atom_modify>` command will turn them off. Atom :doc:`atom_modify id no <atom_modify>` command will turn them off. Atom IDs are required for molecular systems with bond topology (bonds, angles, dihedrals, etc). Thus if you model a molecular system with more than 2 billion atoms, you need the "bigbig" setting. Loading Loading @@ -341,7 +341,7 @@ Read or write compressed files If this option is enabled, large files can be read or written with gzip compression by several LAMMPS commands, including :doc:`read\_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`. :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`. **CMake variables**\ : Loading doc/src/Commands_bond.rst +1 −1 Original line number Diff line number Diff line Loading @@ -131,7 +131,7 @@ OPT. Improper_style potentials ========================= All LAMMPS :doc:`improper\_style <improper_style>` commands. Some styles All LAMMPS :doc:`improper_style <improper_style>` 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. Loading doc/src/Commands_category.rst +45 −45 Original line number Diff line number Diff line Loading @@ -18,73 +18,73 @@ Setup simulation box: * :doc:`boundary <boundary>`, * :doc:`box <box>`, * :doc:`change\_box <change_box>`, * :doc:`create\_box <create_box>`, * :doc:`change_box <change_box>`, * :doc:`create_box <create_box>`, * :doc:`dimension <dimension>`, * :doc:`lattice <lattice>`, * :doc:`region <region>` Setup atoms: * :doc:`atom\_modify <atom_modify>`, * :doc:`atom\_style <atom_style>`, * :doc:`atom_modify <atom_modify>`, * :doc:`atom_style <atom_style>`, * :doc:`balance <balance>`, * :doc:`create\_atoms <create_atoms>`, * :doc:`create\_bonds <create_bonds>`, * :doc:`delete\_atoms <delete_atoms>`, * :doc:`delete\_bonds <delete_bonds>`, * :doc:`displace\_atoms <displace_atoms>`, * :doc:`create_atoms <create_atoms>`, * :doc:`create_bonds <create_bonds>`, * :doc:`delete_atoms <delete_atoms>`, * :doc:`delete_bonds <delete_bonds>`, * :doc:`displace_atoms <displace_atoms>`, * :doc:`group <group>`, * :doc:`mass <mass>`, * :doc:`molecule <molecule>`, * :doc:`read\_data <read_data>`, * :doc:`read\_dump <read_dump>`, * :doc:`read\_restart <read_restart>`, * :doc:`read_data <read_data>`, * :doc:`read_dump <read_dump>`, * :doc:`read_restart <read_restart>`, * :doc:`replicate <replicate>`, * :doc:`set <set>`, * :doc:`velocity <velocity>` Force fields: * :doc:`angle\_coeff <angle_coeff>`, * :doc:`angle\_style <angle_style>`, * :doc:`bond\_coeff <bond_coeff>`, * :doc:`bond\_style <bond_style>`, * :doc:`bond\_write <bond_write>`, * :doc:`angle_coeff <angle_coeff>`, * :doc:`angle_style <angle_style>`, * :doc:`bond_coeff <bond_coeff>`, * :doc:`bond_style <bond_style>`, * :doc:`bond_write <bond_write>`, * :doc:`dielectric <dielectric>`, * :doc:`dihedral\_coeff <dihedral_coeff>`, * :doc:`dihedral\_style <dihedral_style>`, * :doc:`improper\_coeff <improper_coeff>`, * :doc:`improper\_style <improper_style>`, * :doc:`kspace\_modify <kspace_modify>`, * :doc:`kspace\_style <kspace_style>`, * :doc:`pair\_coeff <pair_coeff>`, * :doc:`pair\_modify <pair_modify>`, * :doc:`pair\_style <pair_style>`, * :doc:`pair\_write <pair_write>`, * :doc:`special\_bonds <special_bonds>` * :doc:`dihedral_coeff <dihedral_coeff>`, * :doc:`dihedral_style <dihedral_style>`, * :doc:`improper_coeff <improper_coeff>`, * :doc:`improper_style <improper_style>`, * :doc:`kspace_modify <kspace_modify>`, * :doc:`kspace_style <kspace_style>`, * :doc:`pair_coeff <pair_coeff>`, * :doc:`pair_modify <pair_modify>`, * :doc:`pair_style <pair_style>`, * :doc:`pair_write <pair_write>`, * :doc:`special_bonds <special_bonds>` Settings: * :doc:`comm\_modify <comm_modify>`, * :doc:`comm\_style <comm_style>`, * :doc:`comm_modify <comm_modify>`, * :doc:`comm_style <comm_style>`, * :doc:`info <info>`, * :doc:`min\_modify <min_modify>`, * :doc:`min\_style <min_style>`, * :doc:`neigh\_modify <neigh_modify>`, * :doc:`min_modify <min_modify>`, * :doc:`min_style <min_style>`, * :doc:`neigh_modify <neigh_modify>`, * :doc:`neighbor <neighbor>`, * :doc:`partition <partition>`, * :doc:`reset\_timestep <reset_timestep>`, * :doc:`run\_style <run_style>`, * :doc:`reset_timestep <reset_timestep>`, * :doc:`run_style <run_style>`, * :doc:`timer <timer>`, * :doc:`timestep <timestep>` Operations within timestepping (fixes) and diagnostics (computes): * :doc:`compute <compute>`, * :doc:`compute\_modify <compute_modify>`, * :doc:`compute_modify <compute_modify>`, * :doc:`fix <fix>`, * :doc:`fix\_modify <fix_modify>`, * :doc:`fix_modify <fix_modify>`, * :doc:`uncompute <uncompute>`, * :doc:`unfix <unfix>` Loading @@ -93,22 +93,22 @@ Output: * :doc:`dump image <dump_image>`, * :doc:`dump movie <dump_image>`, * :doc:`dump <dump>`, * :doc:`dump\_modify <dump_modify>`, * :doc:`dump_modify <dump_modify>`, * :doc:`restart <restart>`, * :doc:`thermo <thermo>`, * :doc:`thermo\_modify <thermo_modify>`, * :doc:`thermo\_style <thermo_style>`, * :doc:`thermo_modify <thermo_modify>`, * :doc:`thermo_style <thermo_style>`, * :doc:`undump <undump>`, * :doc:`write\_coeff <write_coeff>`, * :doc:`write\_data <write_data>`, * :doc:`write\_dump <write_dump>`, * :doc:`write\_restart <write_restart>` * :doc:`write_coeff <write_coeff>`, * :doc:`write_data <write_data>`, * :doc:`write_dump <write_dump>`, * :doc:`write_restart <write_restart>` Actions: * :doc:`minimize <minimize>`, * :doc:`neb <neb>`, * :doc:`neb\_spin <neb_spin>`, * :doc:`neb_spin <neb_spin>`, * :doc:`prd <prd>`, * :doc:`rerun <rerun>`, * :doc:`run <run>`, Loading doc/src/Commands_input.rst +1 −1 Original line number Diff line number Diff line Loading @@ -45,7 +45,7 @@ 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 :doc:`read\_data <read_data>` command initializes the system by setting :doc:`read_data <read_data>` command initializes the system by setting up the simulation box and assigning atoms to processors. If default values are not desired, the :doc:`processors <processors>` and :doc:`boundary <boundary>` commands need to be used before read\_data to Loading Loading
doc/src/Build_extras.rst +1 −1 Original line number Diff line number Diff line Loading @@ -177,7 +177,7 @@ KIM package To build with this package, the KIM library with API v2 must be downloaded and built on your system. It must include the KIM models that you want to use with LAMMPS. If you want to use the :doc:`kim\_query <kim_commands>` use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>` command, you also need to have libcurl installed with the matching development headers and the curl-config tool. Loading
doc/src/Build_settings.rst +6 −6 Original line number Diff line number Diff line Loading @@ -5,11 +5,11 @@ LAMMPS can be built with several optional settings. Each sub-section explain how to do this for building both with CMake and make. | :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS | :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command | :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command | :ref:`Size of LAMMPS data types <size>` | :ref:`Read or write compressed files <gzip>` | :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command | :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command | :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command | :ref:`Memory allocation alignment <align>` | :ref:`Workaround for long long integers <longlong>` | :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library Loading Loading @@ -66,7 +66,7 @@ FFT library --------------------- When the KSPACE package is included in a LAMMPS build, the :doc:`kspace\_style pppm <kspace_style>` command performs 3d FFTs which :doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which require use of an FFT library to compute 1d FFTs. The KISS FFT library is included with LAMMPS but other libraries can be faster. LAMMPS can use them if they are available on your system. Loading Loading @@ -134,7 +134,7 @@ However, note that long-range Coulombics are only a portion of the per-timestep CPU cost, FFTs are only a portion of long-range Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel communication can be costly). A breakdown of these timings is printed to the screen at the end of a run using the :doc:`kspace\_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>` to the screen at the end of a run using the :doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>` doc page gives more details. FFTW is a fast, portable FFT library that should also work on any Loading Loading @@ -235,7 +235,7 @@ support 8-byte integers. It allows for: Atom IDs are not required for atomic systems which do not store bond topology information, though IDs are enabled by default. The :doc:`atom\_modify id no <atom_modify>` command will turn them off. Atom :doc:`atom_modify id no <atom_modify>` command will turn them off. Atom IDs are required for molecular systems with bond topology (bonds, angles, dihedrals, etc). Thus if you model a molecular system with more than 2 billion atoms, you need the "bigbig" setting. Loading Loading @@ -341,7 +341,7 @@ Read or write compressed files If this option is enabled, large files can be read or written with gzip compression by several LAMMPS commands, including :doc:`read\_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`. :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`. **CMake variables**\ : Loading
doc/src/Commands_bond.rst +1 −1 Original line number Diff line number Diff line Loading @@ -131,7 +131,7 @@ OPT. Improper_style potentials ========================= All LAMMPS :doc:`improper\_style <improper_style>` commands. Some styles All LAMMPS :doc:`improper_style <improper_style>` 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. Loading
doc/src/Commands_category.rst +45 −45 Original line number Diff line number Diff line Loading @@ -18,73 +18,73 @@ Setup simulation box: * :doc:`boundary <boundary>`, * :doc:`box <box>`, * :doc:`change\_box <change_box>`, * :doc:`create\_box <create_box>`, * :doc:`change_box <change_box>`, * :doc:`create_box <create_box>`, * :doc:`dimension <dimension>`, * :doc:`lattice <lattice>`, * :doc:`region <region>` Setup atoms: * :doc:`atom\_modify <atom_modify>`, * :doc:`atom\_style <atom_style>`, * :doc:`atom_modify <atom_modify>`, * :doc:`atom_style <atom_style>`, * :doc:`balance <balance>`, * :doc:`create\_atoms <create_atoms>`, * :doc:`create\_bonds <create_bonds>`, * :doc:`delete\_atoms <delete_atoms>`, * :doc:`delete\_bonds <delete_bonds>`, * :doc:`displace\_atoms <displace_atoms>`, * :doc:`create_atoms <create_atoms>`, * :doc:`create_bonds <create_bonds>`, * :doc:`delete_atoms <delete_atoms>`, * :doc:`delete_bonds <delete_bonds>`, * :doc:`displace_atoms <displace_atoms>`, * :doc:`group <group>`, * :doc:`mass <mass>`, * :doc:`molecule <molecule>`, * :doc:`read\_data <read_data>`, * :doc:`read\_dump <read_dump>`, * :doc:`read\_restart <read_restart>`, * :doc:`read_data <read_data>`, * :doc:`read_dump <read_dump>`, * :doc:`read_restart <read_restart>`, * :doc:`replicate <replicate>`, * :doc:`set <set>`, * :doc:`velocity <velocity>` Force fields: * :doc:`angle\_coeff <angle_coeff>`, * :doc:`angle\_style <angle_style>`, * :doc:`bond\_coeff <bond_coeff>`, * :doc:`bond\_style <bond_style>`, * :doc:`bond\_write <bond_write>`, * :doc:`angle_coeff <angle_coeff>`, * :doc:`angle_style <angle_style>`, * :doc:`bond_coeff <bond_coeff>`, * :doc:`bond_style <bond_style>`, * :doc:`bond_write <bond_write>`, * :doc:`dielectric <dielectric>`, * :doc:`dihedral\_coeff <dihedral_coeff>`, * :doc:`dihedral\_style <dihedral_style>`, * :doc:`improper\_coeff <improper_coeff>`, * :doc:`improper\_style <improper_style>`, * :doc:`kspace\_modify <kspace_modify>`, * :doc:`kspace\_style <kspace_style>`, * :doc:`pair\_coeff <pair_coeff>`, * :doc:`pair\_modify <pair_modify>`, * :doc:`pair\_style <pair_style>`, * :doc:`pair\_write <pair_write>`, * :doc:`special\_bonds <special_bonds>` * :doc:`dihedral_coeff <dihedral_coeff>`, * :doc:`dihedral_style <dihedral_style>`, * :doc:`improper_coeff <improper_coeff>`, * :doc:`improper_style <improper_style>`, * :doc:`kspace_modify <kspace_modify>`, * :doc:`kspace_style <kspace_style>`, * :doc:`pair_coeff <pair_coeff>`, * :doc:`pair_modify <pair_modify>`, * :doc:`pair_style <pair_style>`, * :doc:`pair_write <pair_write>`, * :doc:`special_bonds <special_bonds>` Settings: * :doc:`comm\_modify <comm_modify>`, * :doc:`comm\_style <comm_style>`, * :doc:`comm_modify <comm_modify>`, * :doc:`comm_style <comm_style>`, * :doc:`info <info>`, * :doc:`min\_modify <min_modify>`, * :doc:`min\_style <min_style>`, * :doc:`neigh\_modify <neigh_modify>`, * :doc:`min_modify <min_modify>`, * :doc:`min_style <min_style>`, * :doc:`neigh_modify <neigh_modify>`, * :doc:`neighbor <neighbor>`, * :doc:`partition <partition>`, * :doc:`reset\_timestep <reset_timestep>`, * :doc:`run\_style <run_style>`, * :doc:`reset_timestep <reset_timestep>`, * :doc:`run_style <run_style>`, * :doc:`timer <timer>`, * :doc:`timestep <timestep>` Operations within timestepping (fixes) and diagnostics (computes): * :doc:`compute <compute>`, * :doc:`compute\_modify <compute_modify>`, * :doc:`compute_modify <compute_modify>`, * :doc:`fix <fix>`, * :doc:`fix\_modify <fix_modify>`, * :doc:`fix_modify <fix_modify>`, * :doc:`uncompute <uncompute>`, * :doc:`unfix <unfix>` Loading @@ -93,22 +93,22 @@ Output: * :doc:`dump image <dump_image>`, * :doc:`dump movie <dump_image>`, * :doc:`dump <dump>`, * :doc:`dump\_modify <dump_modify>`, * :doc:`dump_modify <dump_modify>`, * :doc:`restart <restart>`, * :doc:`thermo <thermo>`, * :doc:`thermo\_modify <thermo_modify>`, * :doc:`thermo\_style <thermo_style>`, * :doc:`thermo_modify <thermo_modify>`, * :doc:`thermo_style <thermo_style>`, * :doc:`undump <undump>`, * :doc:`write\_coeff <write_coeff>`, * :doc:`write\_data <write_data>`, * :doc:`write\_dump <write_dump>`, * :doc:`write\_restart <write_restart>` * :doc:`write_coeff <write_coeff>`, * :doc:`write_data <write_data>`, * :doc:`write_dump <write_dump>`, * :doc:`write_restart <write_restart>` Actions: * :doc:`minimize <minimize>`, * :doc:`neb <neb>`, * :doc:`neb\_spin <neb_spin>`, * :doc:`neb_spin <neb_spin>`, * :doc:`prd <prd>`, * :doc:`rerun <rerun>`, * :doc:`run <run>`, Loading
doc/src/Commands_input.rst +1 −1 Original line number Diff line number Diff line Loading @@ -45,7 +45,7 @@ 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 :doc:`read\_data <read_data>` command initializes the system by setting :doc:`read_data <read_data>` command initializes the system by setting up the simulation box and assigning atoms to processors. If default values are not desired, the :doc:`processors <processors>` and :doc:`boundary <boundary>` commands need to be used before read\_data to Loading
