make compress yes the default

Syntax

""""""

Syntax

""""""

.. parsed-literal::

   reset_mol_ids group-ID keyword value ...

.. code-block:: LAMMPS

   reset_mol_ids all

   reset_mol_ids all offset 10 single yes compress yes

   reset_mol_ids solvent offset 1000

   reset_mol_ids solvent offset auto

   reset_mol_ids all offset 10 single yes

   reset_mol_ids solvent compress yes offset 100

   reset_mol_ids solvent compress no

Description

"""""""""""

group are reset; molecule IDs for atoms not in the group are not

changed.

For purposes of this operation, molecules are identified by the

current bond connectivity in the system, which may or may not be

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 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.

For purposes of this operation, molecules are identified by the current

bond connectivity in the system, which may or may not be consistent with

the current molecule IDs.  A molecule in this context is a set of atoms

connected to each other with explicit bonds.  The specific algorithm

used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`

Once the molecules are identified and a new molecule ID computed for

each, this command will update the current molecule ID for all atoms in

the group with the new molecule ID.  Note that if the group excludes

atoms within molecules, one (physical) molecule may become two or more

(logical) molecules.  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>`,

has lost molecules, e.g. via the :doc:`fix evaporate <fix_evaporate>`

command.

The *compress* keyword determines how new molecule IDs are assigned.

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

The *compress* keyword determines how new molecule IDs are computed.  If

the setting is *yes* (the default) 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 details on the selecting the range of these values.

the *offset* keyword for details on selecting the range of these values.

If the setting is *no*, the molecule ID of every atom in the molecule

will be set to the smallest atom ID of any atom in the molecule.

The *single* keyword determines whether single atoms (not bonded to

another atom) are treated as one-atom molecules or not, based on the

: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_atoms <delete_atoms>`,

:doc:`compute fragment/atom <compute_cluster_atom>`

**Default:**

Default

"""""""

The default keyword settings are compress = no, single = no, and

The default keyword settings are compress = yes, single = no, and

offset = -1.

  if (igroup == -1) error->all(FLERR,"Could not find reset_mol_ids group ID");

  int groupbit = group->bitmask[igroup];

  int compressflag = 0;

  int compressflag = 1;

  int singleflag = 0;

  tagint offset = -1;