Loading doc/src/Build_extras.rst +10 −3 Original line number Diff line number Diff line Loading @@ -287,22 +287,29 @@ KOKKOS\_ARCH settings described below. Note that for CMake, these are really Kokkos variables, not LAMMPS variables. Hence you must use case-sensitive values, e.g. BDW, not bdw. * AMDAVX = AMD 64-bit x86 CPUs * EPYC = AMD EPYC Zen class CPUs * ARMv80 = ARMv8.0 Compatible CPU * ARMv81 = ARMv8.1 Compatible CPU * ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU * BGQ = IBM Blue Gene/Q CPUs * Power8 = IBM POWER8 CPUs * Power9 = IBM POWER9 CPUs * ARMv8-TX2 = ARMv8 Cavium ThunderX2 CPU * WSM = Intel Westmere CPUs * SNB = Intel Sandy/Ivy Bridge CPUs * HSW = Intel Haswell CPUs * BDW = Intel Broadwell Xeon E-class CPUs * SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512) * KNC = Intel Knights Corner Xeon Phi * KNL = Intel Knights Landing Xeon Phi * BGQ = IBM Blue Gene/Q CPUs * Power7 = IBM POWER8 CPUs * Power8 = IBM POWER8 CPUs * Power9 = IBM POWER9 CPUs * Kepler = NVIDIA Kepler default (generation CC 3.5) * Kepler30 = NVIDIA Kepler generation CC 3.0 * Kepler32 = NVIDIA Kepler generation CC 3.2 * Kepler35 = NVIDIA Kepler generation CC 3.5 * Kepler37 = NVIDIA Kepler generation CC 3.7 * Maxwell = NVIDIA Maxwell default (generation CC 5.0) * Maxwell50 = NVIDIA Maxwell generation CC 5.0 * Maxwell52 = NVIDIA Maxwell generation CC 5.2 * Maxwell53 = NVIDIA Maxwell generation CC 5.3 Loading doc/src/Commands_all.rst +1 −1 Original line number Diff line number Diff line Loading @@ -17,7 +17,7 @@ General commands An alphabetic list of all general LAMMPS commands. .. table_from_list:: :columns: 6 :columns: 5 * :doc:`angle_coeff <angle_coeff>` * :doc:`angle_style <angle_style>` Loading doc/src/Commands_category.rst +126 −98 Original line number Diff line number Diff line Loading @@ -9,133 +9,161 @@ have their own pages where they are listed alphabetically. Initialization: ------------------------------ * :doc:`newton <newton>`, * :doc:`package <package>`, * :doc:`processors <processors>`, * :doc:`suffix <suffix>`, .. table_from_list:: :columns: 5 * :doc:`newton <newton>` * :doc:`package <package>` * :doc:`processors <processors>` * :doc:`suffix <suffix>` * :doc:`units <units>` Setup simulation box: ------------------------------ * :doc:`boundary <boundary>`, * :doc:`box <box>`, * :doc:`change_box <change_box>`, * :doc:`create_box <create_box>`, * :doc:`dimension <dimension>`, * :doc:`lattice <lattice>`, .. table_from_list:: :columns: 4 * :doc:`boundary <boundary>` * :doc:`box <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:`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:`group <group>`, * :doc:`mass <mass>`, * :doc:`molecule <molecule>`, * :doc:`read_data <read_data>`, * :doc:`read_dump <read_dump>`, * :doc:`read_restart <read_restart>`, * :doc:`replicate <replicate>`, * :doc:`set <set>`, .. table_from_list:: :columns: 4 * :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:`group <group>` * :doc:`mass <mass>` * :doc:`molecule <molecule>` * :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:`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>`, .. table_from_list:: :columns: 4 * :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>` Settings: ------------------------------ * :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:`neighbor <neighbor>`, * :doc:`partition <partition>`, * :doc:`reset_timestep <reset_timestep>`, * :doc:`run_style <run_style>`, * :doc:`timer <timer>`, .. table_from_list:: :columns: 4 * :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:`neighbor <neighbor>` * :doc:`partition <partition>` * :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:`fix <fix>`, * :doc:`fix_modify <fix_modify>`, * :doc:`uncompute <uncompute>`, .. table_from_list:: :columns: 4 * :doc:`compute <compute>` * :doc:`compute_modify <compute_modify>` * :doc:`fix <fix>` * :doc:`fix_modify <fix_modify>` * :doc:`uncompute <uncompute>` * :doc:`unfix <unfix>` Output: ------------------------------ * :doc:`dump image <dump_image>`, * :doc:`dump movie <dump_image>`, * :doc:`dump <dump>`, * :doc:`dump_modify <dump_modify>`, * :doc:`restart <restart>`, * :doc:`thermo <thermo>`, * :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>`, .. table_from_list:: :columns: 4 * :doc:`dump image <dump_image>` * :doc:`dump movie <dump_image>` * :doc:`dump <dump>` * :doc:`dump_modify <dump_modify>` * :doc:`restart <restart>` * :doc:`thermo <thermo>` * :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>` Actions: ------------------------------ * :doc:`minimize <minimize>`, * :doc:`neb <neb>`, * :doc:`neb_spin <neb_spin>`, * :doc:`prd <prd>`, * :doc:`rerun <rerun>`, * :doc:`run <run>`, * :doc:`tad <tad>`, .. table_from_list:: :columns: 6 * :doc:`minimize <minimize>` * :doc:`neb <neb>` * :doc:`neb_spin <neb_spin>` * :doc:`prd <prd>` * :doc:`rerun <rerun>` * :doc:`run <run>` * :doc:`tad <tad>` * :doc:`temper <temper>` Input script control: ------------------------------ * :doc:`clear <clear>`, * :doc:`echo <echo>`, * :doc:`if <if>`, * :doc:`include <include>`, * :doc:`jump <jump>`, * :doc:`label <label>`, * :doc:`log <log>`, * :doc:`next <next>`, * :doc:`print <print>`, * :doc:`python <python>`, * :doc:`quit <quit>`, * :doc:`shell <shell>`, .. table_from_list:: :columns: 7 * :doc:`clear <clear>` * :doc:`echo <echo>` * :doc:`if <if>` * :doc:`include <include>` * :doc:`info <info>` * :doc:`jump <jump>` * :doc:`label <label>` * :doc:`log <log>` * :doc:`next <next>` * :doc:`print <print>` * :doc:`python <python>` * :doc:`quit <quit>` * :doc:`shell <shell>` * :doc:`variable <variable>` doc/src/Commands_compute.rst +1 −1 Original line number Diff line number Diff line Loading @@ -20,7 +20,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. .. table_from_list:: :columns: 6 :columns: 5 * :doc:`ackland/atom <compute_ackland_atom>` * :doc:`adf <compute_adf>` Loading doc/src/Commands_fix.rst +1 −1 Original line number Diff line number Diff line Loading @@ -20,7 +20,7 @@ parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. .. table_from_list:: :columns: 6 :columns: 5 * :doc:`adapt <fix_adapt>` * :doc:`adapt/fep <fix_adapt_fep>` Loading Loading
doc/src/Build_extras.rst +10 −3 Original line number Diff line number Diff line Loading @@ -287,22 +287,29 @@ KOKKOS\_ARCH settings described below. Note that for CMake, these are really Kokkos variables, not LAMMPS variables. Hence you must use case-sensitive values, e.g. BDW, not bdw. * AMDAVX = AMD 64-bit x86 CPUs * EPYC = AMD EPYC Zen class CPUs * ARMv80 = ARMv8.0 Compatible CPU * ARMv81 = ARMv8.1 Compatible CPU * ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU * BGQ = IBM Blue Gene/Q CPUs * Power8 = IBM POWER8 CPUs * Power9 = IBM POWER9 CPUs * ARMv8-TX2 = ARMv8 Cavium ThunderX2 CPU * WSM = Intel Westmere CPUs * SNB = Intel Sandy/Ivy Bridge CPUs * HSW = Intel Haswell CPUs * BDW = Intel Broadwell Xeon E-class CPUs * SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512) * KNC = Intel Knights Corner Xeon Phi * KNL = Intel Knights Landing Xeon Phi * BGQ = IBM Blue Gene/Q CPUs * Power7 = IBM POWER8 CPUs * Power8 = IBM POWER8 CPUs * Power9 = IBM POWER9 CPUs * Kepler = NVIDIA Kepler default (generation CC 3.5) * Kepler30 = NVIDIA Kepler generation CC 3.0 * Kepler32 = NVIDIA Kepler generation CC 3.2 * Kepler35 = NVIDIA Kepler generation CC 3.5 * Kepler37 = NVIDIA Kepler generation CC 3.7 * Maxwell = NVIDIA Maxwell default (generation CC 5.0) * Maxwell50 = NVIDIA Maxwell generation CC 5.0 * Maxwell52 = NVIDIA Maxwell generation CC 5.2 * Maxwell53 = NVIDIA Maxwell generation CC 5.3 Loading
doc/src/Commands_all.rst +1 −1 Original line number Diff line number Diff line Loading @@ -17,7 +17,7 @@ General commands An alphabetic list of all general LAMMPS commands. .. table_from_list:: :columns: 6 :columns: 5 * :doc:`angle_coeff <angle_coeff>` * :doc:`angle_style <angle_style>` Loading
doc/src/Commands_category.rst +126 −98 Original line number Diff line number Diff line Loading @@ -9,133 +9,161 @@ have their own pages where they are listed alphabetically. Initialization: ------------------------------ * :doc:`newton <newton>`, * :doc:`package <package>`, * :doc:`processors <processors>`, * :doc:`suffix <suffix>`, .. table_from_list:: :columns: 5 * :doc:`newton <newton>` * :doc:`package <package>` * :doc:`processors <processors>` * :doc:`suffix <suffix>` * :doc:`units <units>` Setup simulation box: ------------------------------ * :doc:`boundary <boundary>`, * :doc:`box <box>`, * :doc:`change_box <change_box>`, * :doc:`create_box <create_box>`, * :doc:`dimension <dimension>`, * :doc:`lattice <lattice>`, .. table_from_list:: :columns: 4 * :doc:`boundary <boundary>` * :doc:`box <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:`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:`group <group>`, * :doc:`mass <mass>`, * :doc:`molecule <molecule>`, * :doc:`read_data <read_data>`, * :doc:`read_dump <read_dump>`, * :doc:`read_restart <read_restart>`, * :doc:`replicate <replicate>`, * :doc:`set <set>`, .. table_from_list:: :columns: 4 * :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:`group <group>` * :doc:`mass <mass>` * :doc:`molecule <molecule>` * :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:`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>`, .. table_from_list:: :columns: 4 * :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>` Settings: ------------------------------ * :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:`neighbor <neighbor>`, * :doc:`partition <partition>`, * :doc:`reset_timestep <reset_timestep>`, * :doc:`run_style <run_style>`, * :doc:`timer <timer>`, .. table_from_list:: :columns: 4 * :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:`neighbor <neighbor>` * :doc:`partition <partition>` * :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:`fix <fix>`, * :doc:`fix_modify <fix_modify>`, * :doc:`uncompute <uncompute>`, .. table_from_list:: :columns: 4 * :doc:`compute <compute>` * :doc:`compute_modify <compute_modify>` * :doc:`fix <fix>` * :doc:`fix_modify <fix_modify>` * :doc:`uncompute <uncompute>` * :doc:`unfix <unfix>` Output: ------------------------------ * :doc:`dump image <dump_image>`, * :doc:`dump movie <dump_image>`, * :doc:`dump <dump>`, * :doc:`dump_modify <dump_modify>`, * :doc:`restart <restart>`, * :doc:`thermo <thermo>`, * :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>`, .. table_from_list:: :columns: 4 * :doc:`dump image <dump_image>` * :doc:`dump movie <dump_image>` * :doc:`dump <dump>` * :doc:`dump_modify <dump_modify>` * :doc:`restart <restart>` * :doc:`thermo <thermo>` * :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>` Actions: ------------------------------ * :doc:`minimize <minimize>`, * :doc:`neb <neb>`, * :doc:`neb_spin <neb_spin>`, * :doc:`prd <prd>`, * :doc:`rerun <rerun>`, * :doc:`run <run>`, * :doc:`tad <tad>`, .. table_from_list:: :columns: 6 * :doc:`minimize <minimize>` * :doc:`neb <neb>` * :doc:`neb_spin <neb_spin>` * :doc:`prd <prd>` * :doc:`rerun <rerun>` * :doc:`run <run>` * :doc:`tad <tad>` * :doc:`temper <temper>` Input script control: ------------------------------ * :doc:`clear <clear>`, * :doc:`echo <echo>`, * :doc:`if <if>`, * :doc:`include <include>`, * :doc:`jump <jump>`, * :doc:`label <label>`, * :doc:`log <log>`, * :doc:`next <next>`, * :doc:`print <print>`, * :doc:`python <python>`, * :doc:`quit <quit>`, * :doc:`shell <shell>`, .. table_from_list:: :columns: 7 * :doc:`clear <clear>` * :doc:`echo <echo>` * :doc:`if <if>` * :doc:`include <include>` * :doc:`info <info>` * :doc:`jump <jump>` * :doc:`label <label>` * :doc:`log <log>` * :doc:`next <next>` * :doc:`print <print>` * :doc:`python <python>` * :doc:`quit <quit>` * :doc:`shell <shell>` * :doc:`variable <variable>`
doc/src/Commands_compute.rst +1 −1 Original line number Diff line number Diff line Loading @@ -20,7 +20,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. .. table_from_list:: :columns: 6 :columns: 5 * :doc:`ackland/atom <compute_ackland_atom>` * :doc:`adf <compute_adf>` Loading
doc/src/Commands_fix.rst +1 −1 Original line number Diff line number Diff line Loading @@ -20,7 +20,7 @@ parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. .. table_from_list:: :columns: 6 :columns: 5 * :doc:`adapt <fix_adapt>` * :doc:`adapt/fep <fix_adapt_fep>` Loading
