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Merge branch 'develop' into collected-small-changes

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Axel Kohlmeyer
2022-11-30 08:52:13 -05:00
parent c11eabddc0 63b2d2eec7
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3
doc/src/Commands_all.rst
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@ -89,8 +89,7 @@ table above.
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_atom_ids <reset_atom_ids>`
* :doc:`reset_mol_ids <reset_mol_ids>`
* :doc:`reset_atoms <reset_atoms>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`

33
doc/src/Commands_removed.rst
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@ -26,10 +26,15 @@ Box command
The *box* command has been removed and the LAMMPS code changed so it won't
be needed. If present, LAMMPS will ignore the command and print a warning.
Reset_ids command
-----------------
Reset_ids, reset_atom_ids, reset_mol_ids commands
-------------------------------------------------
The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
.. deprecated:: TBD
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.
MEAM package
------------
@ -39,18 +44,21 @@ The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
Fortran code of MEAM into C++, which removes several restrictions
(e.g. there can be multiple instances in hybrid pair styles) and allows
for some optimizations leading to better performance. The pair style
:doc:`meam <pair_meam>` has the exact same syntax.
:doc:`meam <pair_meam>` has the exact same syntax. For a transition
period the C++ version of MEAM was called USER-MEAMC so it could
coexist with the Fortran version.
REAX package
------------
The REAX package has been removed since it was superseded by the
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF
package has been tested to yield equivalent results to the REAX package,
offers better performance, supports OpenMP multi-threading via OPENMP,
and GPU and threading parallelization through KOKKOS. The new pair styles
are not syntax compatible with the removed reax pair style, so input
files will have to be adapted.
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF package has been tested
to yield equivalent results to the REAX package, offers better
performance, supports OpenMP multi-threading via OPENMP, and GPU and
threading parallelization through KOKKOS. The new pair styles are not
syntax compatible with the removed reax pair style, so input files will
have to be adapted. The REAXFF package was originally called
USER-REAXC.
USER-CUDA package
-----------------
@ -69,5 +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>`

6
doc/src/Developer_unittest.rst
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@ -226,9 +226,9 @@ The following test programs are currently available:
* - ``test_kim_commands.cpp``
- KimCommands
- Tests for several commands from the :ref:`KIM package <PKG-KIM>`
* - ``test_reset_ids.cpp``
- ResetIDs
- Tests to validate the :doc:`reset_atom_ids <reset_atom_ids>` and :doc:`reset_mol_ids <reset_mol_ids>` commands
* - ``test_reset_atoms.cpp``
- ResetAtoms
- Tests to validate the :doc:`reset_atoms <reset_atoms>` sub-commands
Tests for the C-style library interface

3
doc/src/commands_list.rst
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@ -89,8 +89,7 @@ Commands
region
replicate
rerun
reset_atom_ids
reset_mol_ids
reset_atoms
reset_timestep
restart
run

4
doc/src/delete_atoms.rst
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@ -135,7 +135,7 @@ 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_atom_ids <reset_atom_ids>` command can be used after this
: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
@ -203,7 +203,7 @@ using molecule template files via the :doc:`molecule <molecule>` and
Related commands
""""""""""""""""
:doc:`create_atoms <create_atoms>`, :doc:`reset_atom_ids <reset_atom_ids>`
:doc:`create_atoms <create_atoms>`, :doc:`reset_atoms id <reset_atoms>`
Default
"""""""

12
doc/src/fix_bond_react.rst
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@ -177,12 +177,12 @@ due to the internal dynamic grouping performed by fix bond/react.
If the group-ID is an existing static group, react-group-IDs
should also be specified as this static group or a subset.
The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids <reset_mol_ids>`
command after a reaction occurs, to ensure that molecule IDs are
consistent with the new bond topology. The group-ID used for
:doc:`reset_mol_ids <reset_mol_ids>` is the group-ID for this fix.
Resetting molecule IDs is necessarily a global operation, so it can
be slow for very large systems.
The *reset_mol_ids* keyword invokes the :doc:`reset_atoms mol
<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>` is the group-ID for this
fix. Resetting molecule IDs is necessarily a global operation, so it
can be slow for very large systems.
The following comments pertain to each *react* argument (in other
words, they can be customized for each reaction, or reaction step):

94
doc/src/reset_atom_ids.rst
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@ -1,94 +0,0 @@
.. index:: reset_atom_ids
reset_atom_ids command
======================
Syntax
""""""
.. code-block:: LAMMPS
reset_atom_ids 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_atom_ids
reset_atom_ids sort yes
Description
"""""""""""
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_atom_ids so that subsequent communication is not inefficient.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`delete_atoms <delete_atoms>`
Default
"""""""
By default, *sort* is no.

283
doc/src/reset_atoms.rst Normal file
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@ -0,0 +1,283 @@
.. index:: reset_atoms
reset_atoms command
===================
Syntax
""""""
.. code-block:: LAMMPS
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-ID 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
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 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.
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 different 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
""""""""
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.

116
doc/src/reset_mol_ids.rst
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@ -1,116 +0,0 @@
.. index:: reset_mol_ids
reset_mol_ids command
=====================
Syntax
""""""
.. parsed-literal::
reset_mol_ids 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_mol_ids all
reset_mol_ids all offset 10 single yes
reset_mol_ids solvent compress yes offset 100
reset_mol_ids solvent compress no
Description
"""""""""""
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::
The 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 it
does not perform a full update of the bond topology data structures
within LAMMPS.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`reset_atom_ids <reset_atom_ids>`, :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:`compute fragment/atom <compute_cluster_atom>`
Default
"""""""
The default keyword settings are compress = yes, single = no, and
offset = -1.