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add reset command to docs, adapt pages for sub-commands

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Axel Kohlmeyer 2022-11-17 22:52:07 -05:00
parent 0635a46891
commit c9a6299d28
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6 changed files with 46 additions and 40 deletions
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4
doc/src/Commands_all.rst
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@ -90,9 +90,7 @@ table above.
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_atom_ids <reset_atom_ids>`
* :doc:`reset_image_flags <reset_image_flags>`
* :doc:`reset_mol_ids <reset_mol_ids>`
* :doc:`reset <reset>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`

1
doc/src/commands_list.rst
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@ -90,6 +90,7 @@ Commands
region
replicate
rerun
reset
reset_atom_ids
reset_image_flags
reset_mol_ids

19
doc/src/reset_atom_ids.rst
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@ -1,14 +1,14 @@
.. index:: reset_atom_ids
reset_atom_ids command
======================
reset atom_ids sub-command
==========================
Syntax
""""""
.. code-block:: LAMMPS
reset_atom_ids keyword values ...
reset atom_ids 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 atom_ids
reset atom_ids sort yes
Description
"""""""""""
@ -74,10 +74,11 @@ processor have consecutive IDs, as the :doc:`create_atoms
defined, an error about bond topology atom IDs not being found may
result. This is because the cutoff distance for ghost atom
communication was not sufficient to find atoms in bonds, angles, etc
that are owned by other processors. The :doc:`comm_modify cutoff <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.
that are owned by other processors. The :doc:`comm_modify cutoff
<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.
Restrictions
""""""""""""

30
doc/src/reset_image_flags.rst
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@ -1,14 +1,14 @@
.. index:: reset_image_flags
reset_image_flags command
=========================
reset image_flags sub-command
=============================
Syntax
""""""
.. parsed-literal::
reset_image_flags group-ID
reset image_flags 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 image_flags all
reset image_flags mobile
Description
"""""""""""
@ -38,18 +38,20 @@ the largest and the smallest image flag in each direction across all
atoms in the fragment is computed and subtracted from the current image
flag in the same direction.
This can be a useful operation to perform after running longer equilibration
runs of mobile systems where molecules would pass through the system multiple
times and thus produce non-zero image flags.
This can be a useful operation to perform after running longer
equilibration runs of mobile systems where molecules would pass through
the system multiple times and thus produce non-zero image flags.
.. note::
The same as explained for the :doc:`compute fragment/atom
Same as explained for the :doc:`compute fragment/atom
<compute_cluster_atom>` command, molecules are identified using the
current bond topology. This will not account for bonds broken by
the :doc:`bond_style quartic <bond_quartic>` command because it
does not perform a full update of the bond topology data structures
within LAMMPS.
current bond topology. This will **not** account for bonds broken by
the :doc:`bond_style quartic <bond_quartic>` command, because this
bond style does not perform a full update of the bond topology data
structures within LAMMPS. In that case, using the :doc:`delete_bonds
all bond 0 remove <delete_bonds>` will permanently delete such
broken bonds and should thus be used first.
Restrictions
""""""""""""
@ -59,7 +61,7 @@ The command can only be used when the atom style supports bonds.
Related commands
""""""""""""""""
:doc:`reset_mol_ids <reset_mol_ids>`,
:doc:`reset mol_ids <reset_mol_ids>`,
:doc:`compute fragment/atom <compute_cluster_atom>`
Defaults

29
doc/src/reset_mol_ids.rst
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@ -1,14 +1,14 @@
.. index:: reset_mol_ids
reset_mol_ids command
=====================
reset mol_ids sub-command
=========================
Syntax
""""""
.. parsed-literal::
reset_mol_ids group-ID keyword value ...
reset mol_ids 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 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
Description
"""""""""""
@ -88,12 +88,14 @@ is not *all* there may be collisions with the molecule IDs of other atoms.
.. note::
The same as explained for the :doc:`compute fragment/atom
Same as explained for the :doc:`compute fragment/atom
<compute_cluster_atom>` command, molecules are identified using the
current bond topology. This will not account for bonds broken by
the :doc:`bond_style quartic <bond_quartic>` command because it
does not perform a full update of the bond topology data structures
within LAMMPS.
current bond topology. This will **not** account for bonds broken by
the :doc:`bond_style quartic <bond_quartic>` command, because this
bond style does not perform a full update of the bond topology data
structures within LAMMPS. In that case, using the :doc:`delete_bonds
all bond 0 remove <delete_bonds>` will permanently delete such broken
bonds and should thus be used first.
Restrictions
""""""""""""
@ -102,11 +104,12 @@ none
Related commands
""""""""""""""""
:doc:`reset_atom_ids <reset_atom_ids>`, :doc:`fix bond/react <fix_bond_react>`,
:doc:`reset atom_ids <reset_atom_ids>`, :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>`,
:doc:`delete_atoms <delete_atoms>`,
:doc:`delete_bonds <delete_bonds>`,
:doc:`compute fragment/atom <compute_cluster_atom>`
Default

3
doc/utils/check-styles.py
View File

@ -259,10 +259,11 @@ skip_angle = ('sdk')
skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
skip_pair = ('meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm')
skip_compute = ('pressure/cylinder')
skip_command = ('reset_atom_ids', 'reset_image_flags', 'reset_mol_ids')
counter = 0
counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",command,'Command',suffix=True)
counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",command,'Command',skip=skip_command,suffix=True)
counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",compute,'Compute',skip=skip_compute,suffix=True)
counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",compute,'Compute',skip=skip_compute,suffix=False)
counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",fix,'Fix',skip=skip_fix,suffix=True)