63 lines
1.9 KiB
ReStructuredText
63 lines
1.9 KiB
ReStructuredText
.. index:: reset_ids
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reset_ids command
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=================
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Syntax
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""""""
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.. code-block:: LAMMPS
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reset_ids
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Examples
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""""""""
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.. code-block:: LAMMPS
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reset_ids
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Description
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"""""""""""
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Reset atom IDs for the system, including all the global IDs stored
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for bond, angle, dihedral, improper topology data. This will
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create a set of IDs that are numbered contiguously from 1 to N
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for a N atoms system.
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This can be useful to do after performing a "delete_atoms" command for
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a molecular system. The delete_atoms compress yes option will not
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perform this operation due to the existence of bond topology. It can
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also be useful to do after any simulation which has lost atoms,
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e.g. due to atoms moving outside a simulation box with fixed
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boundaries (see the "boundary command"), or due to evaporation (see
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the "fix evaporate" command).
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Note that the resetting of IDs is not really a compression, where gaps
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in atom IDs are removed by decrementing atom IDs that are larger.
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Instead the IDs for all atoms are erased, and new IDs are assigned so
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that the atoms owned by an individual processor have consecutive IDs,
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as the :doc:`create_atoms <create_atoms>` command explains.
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.. note::
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If this command is used before a :doc:`pair style <pair_style>` is
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defined, an error about bond topology atom IDs not being found may
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result. This is because the cutoff distance for ghost atom
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communication was not sufficient to find atoms in bonds, angles, etc
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that are owned by other processors. The :doc:`comm_modify cutoff <comm_modify>` command can be used to correct this issue.
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Or you can define a pair style before using this command. If you do
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the former, you should unset the comm_modify cutoff after using
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reset_ids so that subsequent communication is not inefficient.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`delete_atoms <delete_atoms>`
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**Default:** none
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