\(\renewcommand{\AA}{\text{Å}}\)
reset_atoms command
Syntax
reset_atoms property arguments ...
property = id or image or mol
additional arguments depend on the property
reset_atoms id keyword value ...
zero or more keyword/value pairs can be appended
keyword = sort
sort value = yes or no
reset_atoms image group-ID
group-ID = ID of group of atoms whose image flags will be reset
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
compress value = yes or no offset value = Noffset >= -1 single value = yes or no to treat single atoms (no bonds) as molecules
Examples
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
New in version 22Dec2022.
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 create_atoms command explains.
Note
If this command is used before a 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 comm_modify cutoff 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 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 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 compute fragment/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 compute fragment/atom command, molecules are identified using the current bond topology. This will not account for bonds broken by the bond_style 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 delete_bonds all bond 0 remove 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 compute fragment/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 fix bond/react, fix bond/create, or fix bond/break, all of which can change molecule topologies. It can also be useful after molecules have been deleted with the delete_atoms command or after a simulation which has lost molecules, e.g. via the 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 compute chunk/atom molecule or fix rigid molecule.
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 compute fragment/atom command, molecules are identified using the current bond topology. This will not account for bonds broken by the bond_style 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 delete_bonds all bond 0 remove 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.
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.