diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index 6c7740f9df..8129ac3d75 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -90,7 +90,7 @@ table above. * :doc:`region ` * :doc:`replicate ` * :doc:`rerun ` - * :doc:`reset ` + * :doc:`reset_atoms ` * :doc:`reset_timestep ` * :doc:`restart ` * :doc:`run ` diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index 1000d11e29..5077bbf1c9 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -17,10 +17,14 @@ ways through the :doc:`compute chunk/atom ` command and then averaging is done using :doc:`fix ave/chunk `. Please refer to the :doc:`chunk HOWTO ` section for an overview. -Reset_ids command ------------------ +Reset_ids, reset_atom_ids, reset_mol_ids commands +------------------------------------------------- -The reset_ids command has been renamed to :doc:`reset_atom_ids `. +.. versionchanged:: TBD + +The *reset_ids* or *reset_atom_ids* commands have been renamed to +:doc:`reset_atoms id `. The *reset_mol_ids* command has +been renamed to :doc:`reset_atoms mol `. MEAM package ------------ @@ -30,18 +34,21 @@ The code in the :ref:`MEAM package ` is a translation of the Fortran code of MEAM into C++, which removes several restrictions (e.g. there can be multiple instances in hybrid pair styles) and allows for some optimizations leading to better performance. The pair style -:doc:`meam ` has the exact same syntax. +:doc:`meam ` has the exact same syntax. For a transition +period the C++ version of MEAM was called USER-MEAMC so it could +coexist with the Fortran version. REAX package ------------ The REAX package has been removed since it was superseded by the -:ref:`REAXFF package `. The REAXFF -package has been tested to yield equivalent results to the REAX package, -offers better performance, supports OpenMP multi-threading via OPENMP, -and GPU and threading parallelization through KOKKOS. The new pair styles -are not syntax compatible with the removed reax pair style, so input -files will have to be adapted. +:ref:`REAXFF package `. The REAXFF package has been tested +to yield equivalent results to the REAX package, offers better +performance, supports OpenMP multi-threading via OPENMP, and GPU and +threading parallelization through KOKKOS. The new pair styles are not +syntax compatible with the removed reax pair style, so input files will +have to be adapted. The REAXFF package was originally called +USER-REAXC. USER-CUDA package ----------------- diff --git a/doc/src/Developer_unittest.rst b/doc/src/Developer_unittest.rst index 820e911a8f..aff6128e9c 100644 --- a/doc/src/Developer_unittest.rst +++ b/doc/src/Developer_unittest.rst @@ -226,9 +226,9 @@ The following test programs are currently available: * - ``test_kim_commands.cpp`` - KimCommands - Tests for several commands from the :ref:`KIM package ` - * - ``test_reset_ids.cpp`` - - ResetIDs - - Tests to validate the :doc:`reset_atom_ids ` and :doc:`reset_mol_ids ` commands + * - ``test_reset_atoms.cpp`` + - ResetAtoms + - Tests to validate the :doc:`reset_atoms ` sub-commands Tests for the C-style library interface diff --git a/doc/src/commands_list.rst b/doc/src/commands_list.rst index 036135e5da..44bb25122b 100644 --- a/doc/src/commands_list.rst +++ b/doc/src/commands_list.rst @@ -90,10 +90,10 @@ Commands region replicate rerun - reset - reset_atom_ids - reset_image_flags - reset_mol_ids + reset_atoms + reset_atoms_id + reset_atoms_image + reset_atoms_mol reset_timestep restart run diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 2fdd152196..5746038760 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -129,14 +129,14 @@ other options listed above. Here is the meaning of the optional keywords. -If the *compress* keyword is set to *yes*, then after atoms are -deleted, then atom IDs are re-assigned so that they run from 1 to the -number of atoms in the system. Note that this is not done for -molecular systems (see the :doc:`atom_style ` command), -regardless of the *compress* setting, since it would foul up the bond -connectivity that has already been assigned. However, the -:doc:`reset_atom_ids ` command can be used after this -command to accomplish the same thing. +If the *compress* keyword is set to *yes*, then after atoms are deleted, +then atom IDs are re-assigned so that they run from 1 to the number of +atoms in the system. Note that this is not done for molecular systems +(see the :doc:`atom_style ` command), regardless of the +*compress* setting, since it would foul up the bond connectivity that +has already been assigned. However, the :doc:`reset_atoms id +` command can be used after this command to accomplish +the same thing. Note that the re-assignment of IDs is not really a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. @@ -203,7 +203,7 @@ using molecule template files via the :doc:`molecule ` and Related commands """""""""""""""" -:doc:`create_atoms `, :doc:`reset_atom_ids ` +:doc:`create_atoms `, :doc:`reset_atoms id ` Default """"""" diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 15098761cc..7dcf180346 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -177,12 +177,12 @@ due to the internal dynamic grouping performed by fix bond/react. If the group-ID is an existing static group, react-group-IDs should also be specified as this static group or a subset. -The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids ` -command after a reaction occurs, to ensure that molecule IDs are -consistent with the new bond topology. The group-ID used for -:doc:`reset_mol_ids ` is the group-ID for this fix. -Resetting molecule IDs is necessarily a global operation, so it can -be slow for very large systems. +The *reset_mol_ids* keyword invokes the :doc:`reset_atoms mol +` command after a reaction occurs, to ensure that +molecule IDs are consistent with the new bond topology. The group-ID +used for :doc:`reset_atoms mol ` is the group-ID for this +fix. Resetting molecule IDs is necessarily a global operation, so it +can be slow for very large systems. The following comments pertain to each *react* argument (in other words, they can be customized for each reaction, or reaction step): diff --git a/doc/src/reset.rst b/doc/src/reset_atoms.rst similarity index 62% rename from doc/src/reset.rst rename to doc/src/reset_atoms.rst index cf288bb6f4..aea431e90a 100644 --- a/doc/src/reset.rst +++ b/doc/src/reset_atoms.rst @@ -1,16 +1,16 @@ -.. index:: reset +.. index:: reset_atoms -reset command -============= +reset_atoms command +=================== Syntax """""" .. code-block:: LAMMPS - reset sub-command keyword values ... + reset_atoms sub-command keyword values ... - * sub-command = *atom_ids* or *image_flags* or *mol_ids* + * sub-command = *id* or *image* or *mol* * zero or more keyword/value pairs may be appended depending on sub-command Examples @@ -18,16 +18,16 @@ Examples .. code-block:: LAMMPS - reset atom_ids - reset image_flags all - reset mol_ids all + reset_atoms id + reset_atoms image all + reset_atoms mol all Description """"""""""" .. versionadded:: TBD -The *reset* command provides a number of sub-commands that reset +The *reset_atoms* command provides a number of sub-commands that reset selected atom properties like atom IDs, molecule IDs, or image flags according to selected algorithms. Those are often useful when the simulated system has undergone some significant modifications like @@ -35,9 +35,9 @@ adding or removing atoms or molecules, joining data files, changing bonds, or diffusion. Follow the links listed below to see the documentation for individual sub-commands. -- :doc:`reset_atom_ids` -- :doc:`reset_image_flags` -- :doc:`reset_mol_ids` +- :doc:`reset_atoms_id` +- :doc:`reset_atoms_image` +- :doc:`reset_atoms_mol` Defaults diff --git a/doc/src/reset_atom_ids.rst b/doc/src/reset_atoms_id.rst similarity index 90% rename from doc/src/reset_atom_ids.rst rename to doc/src/reset_atoms_id.rst index d64c248bb0..27378afe55 100644 --- a/doc/src/reset_atom_ids.rst +++ b/doc/src/reset_atoms_id.rst @@ -1,6 +1,6 @@ -.. index:: reset_atom_ids +.. index:: reset_atoms id -reset atom_ids sub-command +reset_atoms id sub-command ========================== Syntax @@ -8,7 +8,7 @@ Syntax .. code-block:: LAMMPS - reset atom_ids keyword values ... + reset_atoms id keyword values ... * zero or more keyword/value pairs may be appended * keyword = *sort* @@ -22,8 +22,8 @@ Examples .. code-block:: LAMMPS - reset atom_ids - reset atom_ids sort yes + reset_atoms id + reset_atoms id sort yes Description """"""""""" @@ -80,7 +80,7 @@ processor have consecutive IDs, as the :doc:`create_atoms ` command can be used to correct this issue. Or you can define a pair style before using this command. If you do the former, you should unset the *comm_modify cutoff* after using *reset - atom_ids* so that subsequent communication is not inefficient. + atoms id* so that subsequent communication is not inefficient. Restrictions """""""""""" @@ -89,7 +89,8 @@ none Related commands """""""""""""""" -:doc:`delete_atoms ` +:doc:`delete_atoms `, :doc:`reset_atoms `, +:doc:`reset_atoms mol ` Default """"""" diff --git a/doc/src/reset_image_flags.rst b/doc/src/reset_atoms_image.rst similarity index 91% rename from doc/src/reset_image_flags.rst rename to doc/src/reset_atoms_image.rst index 5823361468..310c754f9b 100644 --- a/doc/src/reset_image_flags.rst +++ b/doc/src/reset_atoms_image.rst @@ -1,6 +1,6 @@ -.. index:: reset_image_flags +.. index:: reset_atoms image -reset image_flags sub-command +reset_atoms image sub-command ============================= Syntax @@ -8,7 +8,7 @@ Syntax .. parsed-literal:: - reset image_flags group-ID + reset_atoms image group-ID * group-ID = ID of group of atoms whose image flags will be reset @@ -17,8 +17,8 @@ Examples .. code-block:: LAMMPS - reset image_flags all - reset image_flags mobile + reset_atoms image all + reset_atoms image mobile Description """"""""""" @@ -63,7 +63,7 @@ The command can only be used when the atom style supports bonds. Related commands """""""""""""""" -:doc:`reset mol_ids `, +:doc:`reset_atoms `, :doc:`compute fragment/atom ` Defaults diff --git a/doc/src/reset_mol_ids.rst b/doc/src/reset_atoms_mol.rst similarity index 91% rename from doc/src/reset_mol_ids.rst rename to doc/src/reset_atoms_mol.rst index 1005d42a8f..1330cdf9af 100644 --- a/doc/src/reset_mol_ids.rst +++ b/doc/src/reset_atoms_mol.rst @@ -1,14 +1,14 @@ -.. index:: reset_mol_ids +.. index:: reset_atoms mol -reset mol_ids sub-command -========================= +reset_atoms mol sub-command +=========================== Syntax """""" .. parsed-literal:: - reset mol_ids group-ID keyword value ... + reset_atoms mol group-ID keyword value ... * group-ID = ID of group of atoms whose molecule IDs will be reset * zero or more keyword/value pairs may be appended @@ -25,10 +25,10 @@ Examples .. code-block:: LAMMPS - reset mol_ids all - reset mol_ids all offset 10 single yes - reset mol_ids solvent compress yes offset 100 - reset mol_ids solvent compress no + reset_atoms mol all + reset_atoms mol all offset 10 single yes + reset_atoms mol solvent compress yes offset 100 + reset_atoms mol solvent compress no Description """"""""""" @@ -106,7 +106,9 @@ none Related commands """""""""""""""" -:doc:`reset atom_ids `, :doc:`fix bond/react `, +:doc:`reset_atoms `, +:doc:`reset_atoms id `, +:doc:`fix bond/react `, :doc:`fix bond/create `, :doc:`fix bond/break `, :doc:`fix evaporate `,