group command

Syntax

group ID style args
  • ID = user-defined name of the group

  • style = delete 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
    region args = region-ID
    type or id or molecule
      args = list of one or more atom types, atom IDs, or molecule IDs
        any 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 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 every
        region value = region-ID
        var value = name of variable
        every value = N = update group every this many timesteps
    static = no args
    

Examples

group edge region regstrip
group water type 3 4
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 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 3 styles can use arguments specified in one of two formats.

The first format is a list of values (types or IDs). For example, the 2nd command in the examples above puts all atoms of type 3 or 4 into the group named water. Each 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 10,25,50 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, ... 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 3rd 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 4th example above adds all atoms belonging to molecules with IDs from 50 to 250 (inclusive) to the group named polyA.

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 2 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

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

are necessary to insure 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 insures 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 doc page for more details on insuring 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 2nd 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 1st 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.

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 the initial stage of velocity Verlet time integration has been performed, and before neighbor lists or forces are computed. This is the point in the timestep where atom positions have just changed due to the time integration, so the region criterion should be accurate, if applied.

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 mail list and we can change it.

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.

Default

All atoms belong to the “all” group.