group command — LAMMPS documentation

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# group command

## Syntax

    group ID style args

- ID = user-defined name of the group

- style = delete or clear or empty or region or type or id or molecule or variable or include or subtract or union or intersect or dynamic or static

      delete = no args
      clear = no args
      empty = no args
      region args = region-ID
      type or id or molecule
        args = list of one or more atom types (1-Ntypes or type label), atom IDs, or molecule IDs
          any numeric entry in list can be a sequence formatted as A:B or A:B:C where
          A = starting index, B = ending index,
          C = increment between indices, 1 if not specified
        args = logical value
          logical = "<" or "<=" or ">" or ">=" or "==" or "!="
          value = an atom type (1-Ntypes or type label) or atom ID or molecule ID (depending on style)
        args = logical value1 value2
          logical = "<>"
          value1,value2 = atom types or atom IDs or molecule IDs (depending on style)
      variable args = variable-name
      include args = molecule
        molecule = add atoms to group with same molecule ID as atoms already in group
      subtract args = two or more group IDs
      union args = one or more group IDs
      intersect args = two or more group IDs
      dynamic args = parent-ID keyword value ...
        one or more keyword/value pairs may be appended
        keyword = region or var or property or every
          region value = region-ID
          var value = name of variable
          property value = name of custom integer or floating point vector
          every value = N = update group every this many timesteps
      static = no args

## Examples

    group edge region regstrip
    group water type 3 4
    group water type OW HT
    group sub id 10 25 50
    group sub id 10 25 50 500:1000
    group sub id 100:10000:10
    group sub id <= 150
    group polyA molecule <> 50 250
    group hienergy variable eng
    group hienergy include molecule
    group boundary subtract all a2 a3
    group boundary union lower upper
    group boundary intersect upper flow
    group boundary delete
    group mine dynamic all region myRegion every 100

## Description

Identify a collection of atoms as belonging to a group. The group ID can then be used in other commands such as fix, compute, dump, or velocity to act on those atoms together.

If the group ID already exists, the group command adds the specified atoms to the group.

Note

By default groups are static, meaning the atoms are permanently assigned to the group. For example, if the region style is used to assign atoms to a group, the atoms will remain in the group even if they later move out of the region. As explained below, the dynamic style can be used to make a group dynamic so that a periodic determination is made as to which atoms are in the group. Since many LAMMPS commands operate on groups of atoms, you should think carefully about whether making a group dynamic makes sense for your model.

A group with the ID all is predefined. All atoms belong to this group. This group cannot be deleted, or made dynamic.

The delete style removes the named group and un-assigns all atoms that were assigned to that group. Since there is a restriction (see below) that no more than 32 groups can be defined at any time, the delete style allows you to remove groups that are no longer needed, so that more can be specified. You cannot delete a group if it has been used to define a current fix or compute or dump.

The clear style un-assigns all atoms that were assigned to that group. This may be dangerous to do during a simulation run (e.g., using the run every command if a fix or compute or other operation expects the atoms in the group to remain constant), but LAMMPS does not check for this.

The empty style creates an empty group, which is useful for commands like fix gcmc or with complex scripts that add atoms to a group.

The region style puts all atoms in the region volume into the group. Note that this is a static one-time assignment. The atoms remain assigned (or not assigned) to the group even in they later move out of the region volume.

The type, id, and molecule styles put all atoms with the specified atom types, atom IDs, or molecule IDs into the group. These three styles can use arguments specified in one of two formats.

The first format is a list of values (types or IDs). For example, the second command in the examples above puts all atoms of type 3 or 4 into the group named water. Each numeric entry in the list can be a colon-separated sequence `A:B` or `A:B:C`, as in two of the examples above. A “sequence” generates a sequence of values (types or IDs), with an optional increment. The first example with `500:1000` has the default increment of 1 and would add all atom IDs from 500 to 1000 (inclusive) to the group sub, along with 10, 25, and 50 since they also appear in the list of values. The second example with `100:10000:10` uses an increment of 10 and would thus would add atoms IDs \(100, 110, 120, \dots, 9990, 10000\) to the group sub.

The second format is a logical followed by one or two values (type or ID). The 7 valid logicals are listed above. All the logicals except `<>` take a single argument. The third example above adds all atoms with IDs from 1 to 150 to the group named sub. The logical `<>` means “between” and takes 2 arguments. The fourth example above adds all atoms belonging to molecules with IDs from 50 to 250 (inclusive) to the group named polyA. For the type style, type labels are converted into numeric types before being evaluated.

The variable style evaluates a variable to determine which atoms to add to the group. It must be an atom-style variable previously defined in the input script. If the variable evaluates to a non-zero value for a particular atom, then that atom is added to the specified group.

Atom-style variables can specify formulas that include thermodynamic quantities, per-atom values such as atom coordinates, or per-atom quantities calculated by computes, fixes, or other variables. They can also include Boolean logic where two numeric values are compared to yield a 1 or 0 (effectively a true or false). Thus, using the variable style is a general way to flag specific atoms to include or exclude from a group.

For example, these lines define a variable “eatom” that calculates the potential energy of each atom and includes it in the group if its potential energy is above the threshold value \(-3.0\).

    compute         1 all pe/atom
    compute         2 all reduce sum c_1
    thermo_style    custom step temp pe c_2
    run             0 post no

    variable        eatom atom "c_1 > -3.0"
    group           hienergy variable eatom

Note that these lines

    compute         2 all reduce sum c_1
    thermo_style    custom step temp pe c_2
    run             0 post no

are necessary to ensure that the “eatom” variable is current when the group command invokes it. Because the eatom variable computes the per-atom energy via the pe/atom compute, it will only be current if a run has been performed which evaluated pairwise energies, and the pe/atom compute was actually invoked during the run. Printing the thermodynamic info for compute 2 ensures that this is the case, since it sums the pe/atom compute values (in the reduce compute) to output them to the screen. See the “Variable Accuracy” section of the variable page for more details on ensuring that variables are current when they are evaluated between runs.

The include style with its arg molecule adds atoms to a group that have the same molecule ID as atoms already in the group. The molecule ID = 0 is ignored in this operation, since it is assumed to flag isolated atoms that are not part of molecules. An example of where this operation is useful is if the region style has been used previously to add atoms to a group that are within a geometric region. If molecules straddle the region boundary, then atoms outside the region that are part of molecules with atoms inside the region will not be in the group. Using the group command a second time with include molecule will add those atoms that are outside the region to the group.

Note

The include molecule operation is relatively expensive in a parallel sense. This is because it requires communication of relevant molecule IDs between all the processors and each processor to loop over its atoms once per processor, to compare its atoms to the list of molecule IDs from every other processor. Hence it scales as N, rather than N/P as most of the group operations do, where N is the number of atoms, and P is the number of processors.

The subtract style takes a list of two or more existing group names as arguments. All atoms that belong to the first group, but not to any of the other groups are added to the specified group.

The union style takes a list of one or more existing group names as arguments. All atoms that belong to any of the listed groups are added to the specified group.

The intersect style takes a list of two or more existing group names as arguments. Atoms that belong to every one of the listed groups are added to the specified group.

The dynamic style flags an existing or new group as dynamic. This means atoms will be (re)assigned to the group periodically as a simulation runs. This is in contrast to static groups where atoms are permanently assigned to the group. The way the assignment occurs is as follows. Only atoms in the group specified as the parent group via the parent-ID are assigned to the dynamic group before the following conditions are applied.

If the region keyword is used, atoms not in the specified region are removed from the dynamic group.

If the var keyword is used, the variable name must be an atom-style or atomfile-style variable. The variable is evaluated and atoms whose per-atom values are 0.0, are removed from the dynamic group.

If the property keyword is used, the name refers to a custom integer or floating point per-atom vector defined via the fix property/atom command. This means the values in the vector can be read as part of a data file with the read_data command or specified with the set command. Or accessed and changed via the library interface to LAMMPS, or by styles you add to LAMMPS (pair, fix, compute, etc) which access the custom vector and modify its values. Which means the values can be modified between or during simulations. Atoms whose values in the custom vector are zero are removed from the dynamic group. Note that the name of the custom per-atom vector is specified just as name, not as i_name or d_name as it is for other commands that use different kinds of custom atom vectors or arrays as arguments.

The assignment of atoms to a dynamic group is done at the beginning of each run and on every timestep that is a multiple of N, which is the argument for the every keyword (\(N = 1\) is the default). For an energy minimization, via the minimize command, an assignment is made at the beginning of the minimization, but not during the iterations of the minimizer.

The point in the timestep at which atoms are assigned to a dynamic group is after interatomic forces have been computed, but before any fixes which alter forces or otherwise update the system have been invoked. This means that atom positions have been updated, neighbor lists and ghost atoms are current, and both intermolecular and intramolecular forces have been calculated based on the new coordinates. Thus the region criterion, if applied, should be accurate. Also, any computes invoked by an atom-style variable should use updated information for that timestep (e.g., potential energy/atom or coordination number/atom). Similarly, fixes or computes which are invoked after that point in the timestep, should operate on the new group of atoms.

Note

If the region keyword is used to determine what atoms are in the dynamic group, atoms can move outside of the simulation box between reneighboring events. Thus if you want to include all atoms on the left side of the simulation box, you probably want to set the left boundary of the region to be outside the simulation box by some reasonable amount (e.g., up to the cutoff of the potential), else they may be excluded from the dynamic region.

Here is an example of using a dynamic group to shrink the set of atoms being integrated by using a spherical region with a variable radius (shrinking from 18 to 5 over the course of the run). This could be used to model a quench of the system, freezing atoms outside the shrinking sphere, then converting the remaining atoms to a static group and running further.

    variable        nsteps equal 5000
    variable        rad equal 18-(step/v_nsteps)*(18-5)
    region          ss sphere 20 20 0 v_rad
    group           mobile dynamic all region ss
    fix             1 mobile nve
    run             ${nsteps}
    group           mobile static
    run             ${nsteps}

Note

All fixes and computes take a group ID as an argument, but they do not all allow for use of a dynamic group. If you get an error message that this is not allowed, but feel that it should be for the fix or compute in question, then please post your reasoning to the LAMMPS forum at MatSci and we can look into changing it. The same applies if you come across inconsistent behavior when dynamic groups are allowed.

The static style removes the setting for a dynamic group, converting it to a static group (the default). The atoms in the static group are those currently in the dynamic group.

## Restrictions

There can be no more than 32 groups defined at one time, including “all”.

The parent group of a dynamic group cannot itself be a dynamic group.

## Related commands

dump, fix, region, velocity

## Default

All atoms belong to the “all” group.