compute group/group command

Syntax

compute ID group-ID group/group group2-ID keyword value ...
  • ID, group-ID are documented in compute command

  • group/group = style name of this compute command

  • group2-ID = group ID of second (or same) group

  • zero or more keyword/value pairs may be appended

  • keyword = pair or kspace or boundary or molecule

    pair value = yes or no
    kspace value = yes or no
    boundary value = yes or no
    molecule value = off or inter or intra
    

Examples

compute 1 lower group/group upper
compute 1 lower group/group upper kspace yes
compute mine fluid group/group wall

Description

Define a computation that calculates the total energy and force interaction between two groups of atoms: the compute group and the specified group2. The two groups can be the same.

If the pair keyword is set to yes, which is the default, then the the interaction energy will include a pair component which is defined as the pairwise energy between all pairs of atoms where one atom in the pair is in the first group and the other is in the second group. Likewise, the interaction force calculated by this compute will include the force on the compute group atoms due to pairwise interactions with atoms in the specified group2.

Note

The energies computed by the pair keyword do not include tail corrections, even if they are enabled via the pair_modify command.

If the molecule keyword is set to inter or intra than an additional check is made based on the molecule IDs of the two atoms in each pair before including their pairwise interaction energy and force. For the inter setting, the two atoms must be in different molecules. For the intra setting, the two atoms must be in the same molecule.

If the kspace keyword is set to yes, which is not the default, and if a kspace_style is defined, then the interaction energy will include a Kspace component which is the long-range Coulombic energy between all the atoms in the first group and all the atoms in the 2nd group. Likewise, the interaction force calculated by this compute will include the force on the compute group atoms due to long-range Coulombic interactions with atoms in the specified group2.

Normally the long-range Coulombic energy converges only when the net charge of the unit cell is zero. However, one can assume the net charge of the system is neutralized by a uniform background plasma, and a correction to the system energy can be applied to reduce artifacts. For more information see (Bogusz). If the boundary keyword is set to yes, which is the default, and kspace contributions are included, then this energy correction term will be added to the total group-group energy. This correction term does not affect the force calculation and will be zero if one or both of the groups are charge neutral. This energy correction term is the same as that included in the regular Ewald and PPPM routines.

Note

The molecule setting only affects the group/group contributions calculated by the pair keyword. It does not affect the group/group contributions calculated by the kspace keyword.

This compute does not calculate any bond or angle or dihedral or improper interactions between atoms in the two groups.


The pairwise contributions to the group-group interactions are calculated by looping over a neighbor list. The Kspace contribution to the group-group interactions require essentially the same amount of work (FFTs, Ewald summation) as computing long-range forces for the entire system. Thus it can be costly to invoke this compute too frequently.

Note

If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the special_bonds command, and means those pairwise interactions do not appear in the neighbor list. Because this compute uses a neighbor list, it also means those pairs will not be included in the group/group interaction. This does not apply when using long-range coulomb interactions (coul/long, coul/msm, coul/wolf or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the rerun command to compute the group/group interactions for snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in the neighbor list.

If you desire a breakdown of the interactions into a pairwise and Kspace component, simply invoke the compute twice with the appropriate yes/no settings for the pair and kspace keywords. This is no more costly than using a single compute with both keywords set to yes. The individual contributions can be summed in a variable if desired.

This document describes how the long-range group-group calculations are performed.


Output info:

This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. These values can be used by any command that uses global scalar or vector values from a compute as input. See the Howto output doc page for an overview of LAMMPS output options.

Both the scalar and vector values calculated by this compute are “extensive”. The scalar value will be in energy units. The vector values will be in force units.

Restrictions

Not all pair styles can be evaluated in a pairwise mode as required by this compute. For example, 3-body and other many-body potentials, such as Tersoff and Stillinger-Weber cannot be used. EAM potentials only include the pair potential portion of the EAM interaction when used by this compute, not the embedding term.

Not all Kspace styles support calculation of group/group interactions. The ewald and pppm styles do.

Related commands: none

Default

The option defaults are pair = yes, kspace = no, boundary = yes, molecule = off.


Bogusz et al, J Chem Phys, 108, 7070 (1998)