delete_bonds command

Syntax

delete_bonds group-ID style arg keyword ...
  • group-ID = group ID

  • style = multi or atom or bond or angle or dihedral or

    improper or stats

    multi arg = none
    atom arg = an atom type or range of types (see below)
    bond arg = a bond type or range of types (see below)
    angle arg = an angle type or range of types (see below)
    dihedral arg = a dihedral type or range of types (see below)
    improper arg = an improper type or range of types (see below)
    stats arg = none
    
  • zero or more keywords may be appended

  • keyword = any or undo or remove or special

Examples

delete_bonds frozen multi remove
delete_bonds all atom 4 special
delete_bonds all bond 0*3 special
delete_bonds all stats

Description

Turn off (or on) molecular topology interactions, i.e. bonds, angles, dihedrals, impropers. This command is useful for deleting interactions that have been previously turned off by bond-breaking potentials. It is also useful for turning off topology interactions between frozen or rigid atoms. Pairwise interactions can be turned off via the neigh_modify exclude command. The fix shake command also effectively turns off certain bond and angle interactions.

For all styles, by default, an interaction is only turned off (or on) if all the atoms involved are in the specified group. See the any keyword to change the behavior.

Several of the styles (atom, bond, angle, dihedral, improper) take a type as an argument. The specified type should be an integer from 0 to N, where N is the number of relevant types (atom types, bond types, etc). A value of 0 is only relevant for style bond; see details below. In all cases, a wildcard asterisk can be used in place of or in conjunction with the type argument to specify a range of types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the number of types, then an asterisk with no numeric values means all types from 0 to N. A leading asterisk means all types from 0 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). Note that it is fine to include a type of 0 for non-bond styles; it will simply be ignored.

For style multi all bond, angle, dihedral, and improper interactions of any type, involving atoms in the group, are turned off.

Style atom is the same as style multi except that in addition, one or more of the atoms involved in the bond, angle, dihedral, or improper interaction must also be of the specified atom type.

For style bond, only bonds are candidates for turn-off, and the bond must also be of the specified type. Styles angle, dihedral, and improper are treated similarly.

For style bond, you can set the type to 0 to delete bonds that have been previously broken by a bond-breaking potential (which sets the bond type to 0 when a bond is broken); e.g. see the bond_style quartic command.

For style stats no interactions are turned off (or on); the status of all interactions in the specified group is simply reported. This is useful for diagnostic purposes if bonds have been turned off by a bond-breaking potential during a previous run.

The default behavior of the delete_bonds command is to turn off interactions by toggling their type to a negative value, but not to permanently remove the interaction. E.g. a bond_type of 2 is set to -2. The neighbor list creation routines will not include such an interaction in their interaction lists. The default is also to not alter the list of 1-2, 1-3, 1-4 neighbors computed by the special_bonds command and used to weight pairwise force and energy calculations. This means that pairwise computations will proceed as if the bond (or angle, etc) were still turned on.

Several keywords can be appended to the argument list to alter the default behaviors.

The any keyword changes the requirement that all atoms in the bond (angle, etc) must be in the specified group in order to turn-off the interaction. Instead, if any of the atoms in the interaction are in the specified group, it will be turned off (or on if the undo keyword is used).

The undo keyword inverts the delete_bonds command so that the specified bonds, angles, etc are turned on if they are currently turned off. This means a negative value is toggled to positive. For example, for style angle, if type is specified as 2, then all angles with current type = -2, are reset to type = 2. Note that the fix shake command also sets bond and angle types negative, so this option should not be used on those interactions.

The remove keyword is invoked at the end of the delete_bonds operation. It causes turned-off bonds (angles, etc) to be removed from each atom’s data structure and then adjusts the global bond (angle, etc) counts accordingly. Removal is a permanent change; removed bonds cannot be turned back on via the undo keyword. Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list.

The special keyword is invoked at the end of the delete_bonds operation, after (optional) removal. It re-computes the pairwise 1-2, 1-3, 1-4 weighting list. The weighting list computation treats turned-off bonds the same as turned-on. Thus, turned-off bonds must be removed if you wish to change the weighting list.

Note that the choice of remove and special options affects how 1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that have been modified by the delete_bonds command.

Restrictions

This command requires inter-processor communication to acquire ghost atoms, to coordinate the deleting of bonds, angles, etc between atoms shared by multiple processors. This means that your system must be ready to perform a simulation before using this command (force fields setup, atom masses set, etc). Just as would be needed to run dynamics, the force field you define should define a cutoff (e.g. through a pair_style command) which is long enough for a processor to acquire the ghost atoms its needs to compute bond, angle, etc interactions.

If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4 weighting list is not re-computed, this can cause a later fix shake command to fail due to an atom’s bonds being inconsistent with the weighting list. This should only happen if the group used in the fix command includes both atoms in the bond, in which case you probably should be recomputing the weighting list.