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update documentation with new command names

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This commit is contained in:
Axel Kohlmeyer
2022-11-21 17:52:33 -05:00
parent 2b9d5c6c9a
commit cbab8fa102
10 changed files with 77 additions and 67 deletions
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2
doc/src/Commands_all.rst
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@ -90,7 +90,7 @@ table above.
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset <reset>`
* :doc:`reset_atoms <reset_atoms>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`

27
doc/src/Commands_removed.rst
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@ -17,10 +17,14 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` 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 <reset_atom_ids>`.
.. versionchanged:: TBD
The *reset_ids* or *reset_atom_ids* commands have been renamed to
:doc:`reset_atoms id <reset_atoms_id>`. The *reset_mol_ids* command has
been renamed to :doc:`reset_atoms mol <reset_atoms_mol>`.
MEAM package
------------
@ -30,18 +34,21 @@ The code in the :ref:`MEAM package <PKG-MEAM>` 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 <pair_meam>` has the exact same syntax.
:doc:`meam <pair_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The REAX package has been removed since it was superseded by the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 <PKG-REAXFF>`. 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 <PKG-REAXFF>`. 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
-----------------

6
doc/src/Developer_unittest.rst
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@ -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 <PKG-KIM>`
* - ``test_reset_ids.cpp``
- ResetIDs
- Tests to validate the :doc:`reset_atom_ids <reset_atom_ids>` and :doc:`reset_mol_ids <reset_mol_ids>` commands
* - ``test_reset_atoms.cpp``
- ResetAtoms
- Tests to validate the :doc:`reset_atoms <reset_atoms>` sub-commands
Tests for the C-style library interface

8
doc/src/commands_list.rst
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@ -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

18
doc/src/delete_atoms.rst
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@ -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 <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 <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 <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
<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 <molecule>` and
Related commands
""""""""""""""""
:doc:`create_atoms <create_atoms>`, :doc:`reset_atom_ids <reset_atom_ids>`
:doc:`create_atoms <create_atoms>`, :doc:`reset_atoms id <reset_atoms_id>`
Default
"""""""

12
doc/src/fix_bond_react.rst
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@ -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 <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 <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
<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 <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):

24
doc/src/reset.rst → doc/src/reset_atoms.rst
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@ -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

15
doc/src/reset_atom_ids.rst → doc/src/reset_atoms_id.rst
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@ -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
<comm_modify>` 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 <delete_atoms>`
:doc:`delete_atoms <delete_atoms>`, :doc:`reset_atoms <reset_atoms>`,
:doc:`reset_atoms mol <reset_atoms_mol>`
Default
"""""""

12
doc/src/reset_image_flags.rst → doc/src/reset_atoms_image.rst
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@ -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 <reset_mol_ids>`,
:doc:`reset_atoms <reset_atoms>`,
:doc:`compute fragment/atom <compute_cluster_atom>`
Defaults

20
doc/src/reset_mol_ids.rst → doc/src/reset_atoms_mol.rst
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@ -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 <reset_atom_ids>`, :doc:`fix bond/react <fix_bond_react>`,
:doc:`reset_atoms <reset_atoms>`,
:doc:`reset_atoms id <reset_atoms_id>`,
:doc:`fix bond/react <fix_bond_react>`,
:doc:`fix bond/create <fix_bond_create>`,
:doc:`fix bond/break <fix_bond_break>`,
:doc:`fix evaporate <fix_evaporate>`,