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make compress yes the default

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This commit is contained in:
Axel Kohlmeyer
2020-07-09 20:46:45 -04:00
parent 9c97ca11fe
commit 9ec77585ea
2 changed files with 26 additions and 26 deletions
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50
doc/src/reset_mol_ids.rst
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@ -6,9 +6,6 @@ reset_mol_ids command
Syntax
""""""
Syntax
""""""
.. parsed-literal::
reset_mol_ids group-ID keyword value ...
@ -29,9 +26,9 @@ Examples
.. 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
"""""""""""
@ -42,17 +39,18 @@ for atoms in the group. Only molecule IDs for atoms in the specified
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>`,
@ -63,12 +61,12 @@ also be useful after molecules have been deleted with the
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
@ -108,9 +106,11 @@ Related commands
: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.

2
src/reset_mol_ids.cpp
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@ -53,7 +53,7 @@ void ResetMolIDs::command(int narg, char **arg)
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;