# reset_atoms command ## Syntax ``` LAMMPS reset_atoms property arguments ... ``` - property = *id* or *image* or *mol* - additional arguments depend on the property ``` LAMMPS reset_atoms id keyword value ... ``` - zero or more keyword/value pairs can be appended - keyword = *sort* *sort* value = *yes* or *no* ``` LAMMPS reset_atoms image group-ID ``` - group-ID = ID of group of atoms whose image flags will be reset ``` 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* *compress* value = *yes* or *no* *offset* value = *Noffset* >= -1 *single* value = *yes* or *no* to treat single atoms (no bonds) as molecules ## Examples ``` 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 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](create_atoms) command explains. :::: note ::: title Note ::: If this command is used before a [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 [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 [set](set) command. :::: note ::: title 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](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](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 ::: title Note ::: Same as explained for the [compute fragment/atom](compute_cluster_atom) command, molecules are identified using the current bond topology. This will **not** account for bonds broken by the [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 [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 [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 [fix bond/react](fix_bond_react), [fix bond/create](fix_bond_create), or [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 [delete_atoms](delete_atoms) command or after a simulation which has lost molecules, e.g. via the [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 [compute chunk/atom molecule](compute_chunk_atom) or [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 ::: title Note ::: Same as explained for the [compute fragment/atom](compute_cluster_atom) command, molecules are identified using the current bond topology. This will **not** account for bonds broken by the [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 [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 [compute fragment/atom](compute_cluster_atom) [fix bond/react](fix_bond_react), [fix bond/create](fix_bond_create), [fix bond/break](fix_bond_break), [fix evaporate](fix_evaporate), [delete_atoms](delete_atoms), [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.