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simplify formulations a little bit. update example command lines

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Axel Kohlmeyer
2020-07-09 19:52:49 -04:00
parent 4a1acffde9
commit e0e24799c2
1 changed files with 11 additions and 11 deletions
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doc/src/reset_mol_ids.rst
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@ -29,7 +29,7 @@ Examples
.. code-block:: LAMMPS
reset_mol_ids all
reset_mol_ids all offset 10 singlezero
reset_mol_ids all offset 10 single yes compress yes
reset_mol_ids solvent offset 1000
reset_mol_ids solvent offset auto
@ -48,10 +48,11 @@ consistent with current molecule IDs. A molecule is a set of atoms,
each of which is bonded to one or more atoms in the set. Once new
molecules are identified and a molecule ID assigned to each one, this
command will update the current molecule ID for each atom in the group
with a (potentially) new ID. Note that if the group is set so as to
exclude atoms within molecules, one molecule may become several. For
example if the group excludes atoms in the midddle of a linear chain,
then each end of the chain becomes an independent molecules.
with a (potentially) new ID. Note that if the group excludes atoms
within molecules, one molecule may become two or more. For
example if the group excludes atoms in the middle of a linear chain,
then each end of the chain is considered an independent molecule
and will be assigned a different molecule ID.
This can be a useful operation to perform after running reactive
molecular dynamics run with :doc:`fix bond/react <fix_bond_react>`,
@ -67,7 +68,7 @@ If the setting is *no* (the default), the molecule ID of every atom in
the molecule will be set to the smallest atom ID of any atom in the
molecule. If the setting is *yes*, and there are N molecules in the
group, the new molecule IDs will be a set of N contiguous values. See
the *offset* keyword for more details.
the *offset* keyword for details on the selecting the range of these values.
The *single* keyword determines whether single atoms (not bonded to
another atom) are treated as one-atom molecules or not, based on the
@ -81,12 +82,11 @@ The *offset* keyword is only used if the *compress* setting is *yes*.
Its default value is *Noffset* = -1. In that case, if the specified
group is *all*, then the new compressed molecule IDs will range from 1
to N. If the specified group is not *all* and the largest molecule ID
in the non-group atoms is M, then the new compressed molecule IDs will
range from M+1 to M+N, so as to not collide with existing molecule
of atoms outside that group is M, then the new compressed molecule IDs will
range from M+1 to M+N, to avoid collision with existing molecule
IDs. If an *Noffset* >= 0 is specified, then the new compressed
molecule IDs will range from *Noffset*+1 to *Noffset*+N. If the group
is not *all* it is up to you to insure there are no collisions with
the molecule IDs of non-group atoms.
molecule IDs will range from *Noffset*\ +1 to *Noffset*\ +N. If the group
is not *all* there may be collisions with the molecule IDs of other atoms.
.. note::