merged 3 doc pages for reset_atoms command
This commit is contained in:
Steve Plimpton
@ -31,8 +31,8 @@ Reset_ids, reset_atom_ids, reset_mol_ids commands
|
||||
|
||||
.. deprecated:: TBD
|
||||
|
||||
The *reset_ids* or *reset_atom_ids* or *reset_mol_ids* commands have
|
||||
been folded into the :doc:`reset_atoms <reset_atoms>` meta-command. If
|
||||
The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
|
||||
been folded into the :doc:`reset_atoms <reset_atoms>` command. If
|
||||
present, LAMMPS will replace the commands accordingly and print a
|
||||
warning.
|
||||
|
||||
@ -77,5 +77,6 @@ restart2data tool
|
||||
The functionality of the restart2data tool has been folded into the
|
||||
LAMMPS executable directly instead of having a separate tool. A
|
||||
combination of the commands :doc:`read_restart <read_restart>` and
|
||||
:doc:`write_data <write_data>` can be used to the same effect. For added
|
||||
convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
|
||||
:doc:`write_data <write_data>` can be used to the same effect. For
|
||||
added convenience this conversion can also be triggered by
|
||||
:doc:`command line flags <Run_options>`
|
||||
|
||||
@ -90,9 +90,6 @@ Commands
|
||||
replicate
|
||||
rerun
|
||||
reset_atoms
|
||||
reset_atoms_id
|
||||
reset_atoms_image
|
||||
reset_atoms_mol
|
||||
reset_timestep
|
||||
restart
|
||||
run
|
||||
|
||||
@ -129,14 +129,14 @@ other options listed above.
|
||||
|
||||
Here is the meaning of the optional keywords.
|
||||
|
||||
If the *compress* keyword is set to *yes*, then after atoms are deleted,
|
||||
then atom IDs are re-assigned so that they run from 1 to the number of
|
||||
atoms in the system. Note that this is not done for molecular systems
|
||||
(see the :doc:`atom_style <atom_style>` command), regardless of the
|
||||
*compress* setting, since it would foul up the bond connectivity that
|
||||
has already been assigned. However, the :doc:`reset_atoms id
|
||||
<reset_atoms_id>` command can be used after this command to accomplish
|
||||
the same thing.
|
||||
If the *compress* keyword is set to *yes*, then after atoms are
|
||||
deleted, then atom IDs are re-assigned so that they run from 1 to the
|
||||
number of atoms in the system. Note that this is not done for
|
||||
molecular systems (see the :doc:`atom_style <atom_style>` command),
|
||||
regardless of the *compress* setting, since it would foul up the bond
|
||||
connectivity that has already been assigned. However, the
|
||||
:doc:`reset_atoms id <reset_atoms>` command can be used after this
|
||||
command to accomplish the same thing.
|
||||
|
||||
Note that the re-assignment of IDs is not really a compression, where
|
||||
gaps in atom IDs are removed by decrementing atom IDs that are larger.
|
||||
@ -203,7 +203,8 @@ using molecule template files via the :doc:`molecule <molecule>` and
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`create_atoms <create_atoms>`, :doc:`reset_atoms id <reset_atoms_id>`
|
||||
:doc:`create_atoms <create_atoms>`, :doc:`reset_atoms id
|
||||
<reset_atoms>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -178,9 +178,9 @@ due to the internal dynamic grouping performed by fix bond/react.
|
||||
should also be specified as this static group or a subset.
|
||||
|
||||
The *reset_mol_ids* keyword invokes the :doc:`reset_atoms mol
|
||||
<reset_atoms_mol>` command after a reaction occurs, to ensure that
|
||||
<reset_atoms>` command after a reaction occurs, to ensure that
|
||||
molecule IDs are consistent with the new bond topology. The group-ID
|
||||
used for :doc:`reset_atoms mol <reset_atoms_mol>` is the group-ID for this
|
||||
used for :doc:`reset_atoms mol <reset_atoms>` is the group-ID for this
|
||||
fix. Resetting molecule IDs is necessarily a global operation, so it
|
||||
can be slow for very large systems.
|
||||
|
||||
|
||||
@ -8,10 +8,42 @@ Syntax
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_atoms sub-command keyword values ...
|
||||
reset_atoms property arguments ...
|
||||
|
||||
* property = *id* or *image* or *mol*
|
||||
* additional arguments depend on the property
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_atoms *id* keyword value ...
|
||||
|
||||
* zero or more keyword/value pairs can be appended
|
||||
* keyword = *sort*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*sort* value = *yes* or *no*
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_atoms image group-ID
|
||||
|
||||
* group-ID = ID of group of atoms whose image flags will be reset
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset atoms mol group keyword value ...
|
||||
|
||||
* group-ID = ID of group of atoms whose molecule IDs will be reset
|
||||
* zero or more keyword/value pairs can be appended
|
||||
* keyword = *compress* or *offset* or *single*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*compress* value = *yes* or *no*
|
||||
*offset* value = *Noffset* >= -1
|
||||
*single* value = *yes* or *no* to treat single atoms (no bonds) as molecules
|
||||
|
||||
* sub-command = *id* or *image* or *mol*
|
||||
* zero or more keyword/value pairs may be appended depending on sub-command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -19,28 +51,233 @@ Examples
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_atoms id
|
||||
reset_atoms id sort yes
|
||||
reset_atoms image all
|
||||
reset_atoms image mobile
|
||||
reset_atoms mol all
|
||||
reset_atoms mol all offset 10 single yes
|
||||
reset_atoms mol solvent compress yes offset 100
|
||||
reset_atoms mol solvent compress no
|
||||
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
The *reset_atoms* command provides a number of sub-commands that reset
|
||||
selected atom properties like atom IDs, molecule IDs, or image flags
|
||||
according to selected algorithms. Those are often useful when the
|
||||
simulated system has undergone some significant modifications like
|
||||
adding or removing atoms or molecules, joining data files, changing
|
||||
bonds, or diffusion. Follow the links listed below to see the
|
||||
documentation for individual sub-commands.
|
||||
The *reset_atoms* command resets the values of a specified atom
|
||||
property. In contrast to the set command, it does this in a
|
||||
collective manner which resets the values for many atoms in a
|
||||
self-consistent way. This is often useful when the simulated system
|
||||
has undergone significant modifications like adding or removing atoms
|
||||
or molecules, joining data files, changing bonds, or large-scale
|
||||
diffusion.
|
||||
|
||||
- :doc:`reset_atoms_id`
|
||||
- :doc:`reset_atoms_image`
|
||||
- :doc:`reset_atoms_mol`
|
||||
The new values can be thought of as a *reset*, similar to values atoms
|
||||
would have if a new data file were being read or a new simulation
|
||||
performed. Note that the set command also resets atom properties to
|
||||
new values, but it treats each atom independently.
|
||||
|
||||
The *property* setting can be *id* or *image* or *mol*. For *id*, the
|
||||
IDs of all the atoms are reset to contiguous values. For *image*, the
|
||||
image flags of atoms in the specified *group-ID* are reset so that at
|
||||
least one atom in each molecule is in the simulation box (image flag =
|
||||
0). For *mol*, the molecule IDs of all atoms are reset to contiguous
|
||||
values.
|
||||
|
||||
More details on these operations and their arguments or optional
|
||||
keyword/value settings are given below.
|
||||
|
||||
---
|
||||
|
||||
*Property id*
|
||||
|
||||
Reset atom IDs for the entire system, including all the global IDs
|
||||
stored for bond, angle, dihedral, improper topology data. This will
|
||||
create a set of IDs that are numbered contiguously from 1 to N for a N
|
||||
atoms system.
|
||||
|
||||
This can be useful to do after performing a "delete_atoms" command for
|
||||
a molecular system. The delete_atoms compress yes option will not
|
||||
perform this operation due to the existence of bond topology. It can
|
||||
also be useful to do after any simulation which has lost atoms,
|
||||
e.g. due to atoms moving outside a simulation box with fixed
|
||||
boundaries (see the "boundary command"), or due to evaporation (see
|
||||
the "fix evaporate" command).
|
||||
|
||||
If the *sort* keyword is used with a setting of *yes*, then the
|
||||
assignment of new atom IDs will be the same no matter how many
|
||||
processors LAMMPS is running on. This is done by first doing a
|
||||
spatial sort of all the atoms into bins and sorting them within each
|
||||
bin. Because the set of bins is independent of the number of
|
||||
processors, this enables a consistent assignment of new IDs to each
|
||||
atom.
|
||||
|
||||
This can be useful to do after using the "create_atoms" command and/or
|
||||
"replicate" command. In general those commands do not guarantee
|
||||
assignment of the same atom ID to the same physical atom when LAMMPS
|
||||
is run on different numbers of processors. Enforcing consistent IDs
|
||||
can be useful for debugging or comparing output from two different
|
||||
runs.
|
||||
|
||||
Note that the spatial sort requires communication of atom IDs and
|
||||
coordinates between processors in an all-to-all manner. This is done
|
||||
efficiently in LAMMPS, but it is more expensive than how atom IDs are
|
||||
reset without sorting.
|
||||
|
||||
Note that whether sorting or not, the resetting of IDs is not a
|
||||
compression, where gaps in atom IDs are removed by decrementing atom
|
||||
IDs that are larger. Instead the IDs for all atoms are erased, and
|
||||
new IDs are assigned so that the atoms owned by an individual
|
||||
processor have consecutive IDs, as the :doc:`create_atoms
|
||||
<create_atoms>` command explains.
|
||||
|
||||
.. note::
|
||||
|
||||
If this command is used before a :doc:`pair style <pair_style>` is
|
||||
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
|
||||
atoms id* so that subsequent communication is not inefficient.
|
||||
|
||||
---
|
||||
|
||||
*Property image*
|
||||
|
||||
Reset the image flags of atoms so that at least one atom in each
|
||||
molecule has an image flag of 0. Molecular topology is respected so
|
||||
that if the molecule straddles a periodic simulation box boundary, the
|
||||
images flags of all atoms in the molecule will be consistent. This
|
||||
avoids inconsistent image flags that could result from resetting all
|
||||
image flags to zero with the :doc:`set <set>` command.
|
||||
|
||||
.. note::
|
||||
|
||||
If the system has no bonds, there is no reason to use this command,
|
||||
since image flags for differenet atoms do not need to be
|
||||
consistent. Use the :doc:`set <set>` command with its *image*
|
||||
keyword instead.
|
||||
|
||||
Only image flags for atoms in the specified *group-ID* are reset; all
|
||||
others remain unchanged. No check is made for whether the group
|
||||
covers complete molecule fragments and thus whether the command will
|
||||
result in inconsistent image flags.
|
||||
|
||||
Molecular fragments are identified by the algorithm used by the
|
||||
:doc:`compute fragment/atom <compute_cluster_atom>` command. For each
|
||||
fragment the average of 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.
|
||||
|
||||
.. note::
|
||||
|
||||
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 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.
|
||||
|
||||
---
|
||||
|
||||
*Property mol*
|
||||
|
||||
Reset molecule IDs for a specified group of atoms based on current
|
||||
bond connectivity. This will typically create a new set of molecule
|
||||
IDs for atoms in the group. Only molecule IDs for atoms in the
|
||||
specified *group-ID* 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
|
||||
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>`,
|
||||
:doc:`fix bond/create <fix_bond_create>`, or :doc:`fix bond/break
|
||||
<fix_bond_break>`, all of which can change molecule topologies. It can
|
||||
also be useful after molecules have been deleted with the
|
||||
:doc:`delete_atoms <delete_atoms>` command or after a simulation which
|
||||
has lost molecules, e.g. via the :doc:`fix evaporate <fix_evaporate>`
|
||||
command.
|
||||
|
||||
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 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
|
||||
*yes* or *no* setting. If the setting is *no* (the default), their
|
||||
molecule IDs are set to 0. This setting can be important if the new
|
||||
molecule IDs will be used as input to other commands such as
|
||||
:doc:`compute chunk/atom molecule <compute_chunk_atom>` or :doc:`fix
|
||||
rigid molecule <fix_rigid>`.
|
||||
|
||||
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
|
||||
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* there may be collisions with the molecule IDs of other atoms.
|
||||
|
||||
.. note::
|
||||
|
||||
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 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
|
||||
""""""""""""
|
||||
|
||||
The *image* property can only be used when the atom style supports bonds.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`compute fragment/atom <compute_cluster_atom>`
|
||||
: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>`
|
||||
|
||||
Defaults
|
||||
""""""""
|
||||
|
||||
none
|
||||
For property *id*, the default keyword setting is sort = no.
|
||||
|
||||
For property *mol*, the default keyword settings are compress = yes,
|
||||
single = no, and offset = -1.
|
||||
|
||||
@ -1,98 +0,0 @@
|
||||
.. index:: reset_atoms id
|
||||
|
||||
reset_atoms id sub-command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_atoms id keyword values ...
|
||||
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *sort*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*sort* value = *yes* or *no*
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_atoms id
|
||||
reset_atoms id sort yes
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionchanged:: TBD
|
||||
|
||||
Reset atom IDs for the system, including all the global IDs stored
|
||||
for bond, angle, dihedral, improper topology data. This will
|
||||
create a set of IDs that are numbered contiguously from 1 to N
|
||||
for a N atoms system.
|
||||
|
||||
This can be useful to do after performing a "delete_atoms" command for
|
||||
a molecular system. The delete_atoms compress yes option will not
|
||||
perform this operation due to the existence of bond topology. It can
|
||||
also be useful to do after any simulation which has lost atoms,
|
||||
e.g. due to atoms moving outside a simulation box with fixed
|
||||
boundaries (see the "boundary command"), or due to evaporation (see
|
||||
the "fix evaporate" command).
|
||||
|
||||
If the *sort* keyword is used with a setting of *yes*, then the
|
||||
assignment of new atom IDs will be the same no matter how many
|
||||
processors LAMMPS is running on. This is done by first doing a
|
||||
spatial sort of all the atoms into bins and sorting them within each
|
||||
bin. Because the set of bins is independent of the number of
|
||||
processors, this enables a consistent assignment of new IDs to each
|
||||
atom.
|
||||
|
||||
This can be useful to do after using the "create_atoms" command and/or
|
||||
"replicate" command. In general those commands do not guarantee
|
||||
assignment of the same atom ID to the same physical atom when LAMMPS
|
||||
is run on different numbers of processors. Enforcing consistent IDs
|
||||
can be useful for debugging or comparing output from two different
|
||||
runs.
|
||||
|
||||
Note that the spatial sort requires communication of atom IDs and
|
||||
coordinates between processors in an all-to-all manner. This is done
|
||||
efficiently in LAMMPS, but it is more expensive than how atom IDs are
|
||||
reset without sorting.
|
||||
|
||||
Note that whether sorting or not, the resetting of IDs is not a
|
||||
compression, where gaps in atom IDs are removed by decrementing atom
|
||||
IDs that are larger. Instead the IDs for all atoms are erased, and
|
||||
new IDs are assigned so that the atoms owned by an individual
|
||||
processor have consecutive IDs, as the :doc:`create_atoms
|
||||
<create_atoms>` command explains.
|
||||
|
||||
.. note::
|
||||
|
||||
If this command is used before a :doc:`pair style <pair_style>` is
|
||||
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
|
||||
atoms id* so that subsequent communication is not inefficient.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`delete_atoms <delete_atoms>`, :doc:`reset_atoms <reset_atoms>`,
|
||||
:doc:`reset_atoms mol <reset_atoms_mol>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
By default, *sort* is no.
|
||||
@ -1,72 +0,0 @@
|
||||
.. index:: reset_atoms image
|
||||
|
||||
reset_atoms image sub-command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
reset_atoms image group-ID
|
||||
|
||||
* group-ID = ID of group of atoms whose image flags will be reset
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_atoms image all
|
||||
reset_atoms image mobile
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
Reset the image flags of atoms so that molecular fragments with atoms in
|
||||
different periodic images retain their geometry. This avoids
|
||||
inconsistent image flags resulting from resetting them all to zero.
|
||||
|
||||
Only images flags for atoms in the specified group are reset; all others
|
||||
remain unchanged. No check is made whether the group covers complete
|
||||
molecule fragments and thus whether the command will result in
|
||||
inconsistent image flags.
|
||||
|
||||
Molecular fragments are identified by the algorithm used :doc:`compute
|
||||
fragment/atom <compute_cluster_atom>`. For each fragment the average of
|
||||
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.
|
||||
|
||||
.. note::
|
||||
|
||||
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 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
|
||||
""""""""""""
|
||||
|
||||
The command can only be used when the atom style supports bonds.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`reset_atoms <reset_atoms>`,
|
||||
:doc:`compute fragment/atom <compute_cluster_atom>`
|
||||
|
||||
Defaults
|
||||
""""""""
|
||||
|
||||
none
|
||||
@ -1,123 +0,0 @@
|
||||
.. index:: reset_atoms mol
|
||||
|
||||
reset_atoms mol sub-command
|
||||
===========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
reset_atoms mol 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
|
||||
* keyword = *compress* or *offset* or *single*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*compress* value = *yes* or *no*
|
||||
*offset* value = *Noffset* >= -1
|
||||
*single* value = *yes* or *no* to treat single atoms (no bonds) as molecules
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_atoms mol all
|
||||
reset_atoms mol all offset 10 single yes
|
||||
reset_atoms mol solvent compress yes offset 100
|
||||
reset_atoms mol solvent compress no
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionchanged:: TBD
|
||||
|
||||
Reset molecule IDs for a group of atoms based on current bond
|
||||
connectivity. This will typically create a new set of molecule IDs
|
||||
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
|
||||
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>`,
|
||||
:doc:`fix bond/create <fix_bond_create>`, or :doc:`fix bond/break
|
||||
<fix_bond_break>`, all of which can change molecule topologies. It can
|
||||
also be useful after molecules have been deleted with the
|
||||
:doc:`delete_atoms <delete_atoms>` command or after a simulation which
|
||||
has lost molecules, e.g. via the :doc:`fix evaporate <fix_evaporate>`
|
||||
command.
|
||||
|
||||
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 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
|
||||
*yes* or *no* setting. If the setting is *no* (the default), their
|
||||
molecule IDs are set to 0. This setting can be important if the new
|
||||
molecule IDs will be used as input to other commands such as
|
||||
:doc:`compute chunk/atom molecule <compute_chunk_atom>` or :doc:`fix
|
||||
rigid molecule <fix_rigid>`.
|
||||
|
||||
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
|
||||
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* there may be collisions with the molecule IDs of other atoms.
|
||||
|
||||
.. note::
|
||||
|
||||
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 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
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`reset_atoms <reset_atoms>`,
|
||||
:doc:`reset_atoms id <reset_atoms_id>`,
|
||||
: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
|
||||
"""""""
|
||||
|
||||
The default keyword settings are compress = yes, single = no, and
|
||||
offset = -1.
|
||||
Reference in New Issue
Block a user