forked from lijiext/lammps
155 lines
6.8 KiB
Plaintext
155 lines
6.8 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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delete_bonds command :h3
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[Syntax:]
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delete_bonds group-ID style arg keyword ... :pre
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group-ID = group ID :ulb,l
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style = {multi} or {atom} or {bond} or {angle} or {dihedral} or
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{improper} or {stats} :l
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{multi} arg = none
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{atom} arg = an atom type or range of types (see below)
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{bond} arg = a bond type or range of types (see below)
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{angle} arg = an angle type or range of types (see below)
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{dihedral} arg = a dihedral type or range of types (see below)
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{improper} arg = an improper type or range of types (see below)
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{stats} arg = none :pre
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zero or more keywords may be appended :l
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keyword = {any} or {undo} or {remove} or {special} :l
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:ule
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[Examples:]
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delete_bonds frozen multi remove
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delete_bonds all atom 4 special
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delete_bonds all bond 0*3 special
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delete_bonds all stats :pre
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[Description:]
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Turn off (or on) molecular topology interactions, i.e. bonds, angles,
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dihedrals, impropers. This command is useful for deleting
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interactions that have been previously turned off by bond-breaking
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potentials. It is also useful for turning off topology interactions
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between frozen or rigid atoms. Pairwise interactions can be turned
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off via the "neigh_modify exclude"_neigh_modify.html command. The
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"fix shake"_fix_shake.html command also effectively turns off certain
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bond and angle interactions.
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For all styles, by default, an interaction is only turned off (or on)
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if all the atoms involved are in the specified group. See the {any}
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keyword to change the behavior.
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Several of the styles ({atom}, {bond}, {angle}, {dihedral},
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{improper}) take a {type} as an argument. The specified {type} should
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be an integer from 0 to N, where N is the number of relevant types
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(atom types, bond types, etc). A value of 0 is only relevant for
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style {bond}; see details below. In all cases, a wildcard asterisk
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can be used in place of or in conjunction with the {type} argument to
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specify a range of types. This takes the form "*" or "*n" or "n*" or
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"m*n". If N = the number of types, then an asterisk with no numeric
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values means all types from 0 to N. A leading asterisk means all
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types from 0 to n (inclusive). A trailing asterisk means all types
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from n to N (inclusive). A middle asterisk means all types from m to
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n (inclusive). Note that it is fine to include a type of 0 for
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non-bond styles; it will simply be ignored.
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For style {multi} all bond, angle, dihedral, and improper interactions
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of any type, involving atoms in the group, are turned off.
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Style {atom} is the same as style {multi} except that in addition, one
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or more of the atoms involved in the bond, angle, dihedral, or
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improper interaction must also be of the specified atom type.
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For style {bond}, only bonds are candidates for turn-off, and the bond
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must also be of the specified type. Styles {angle}, {dihedral}, and
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{improper} are treated similarly.
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For style {bond}, you can set the type to 0 to delete bonds that have
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been previously broken by a bond-breaking potential (which sets the
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bond type to 0 when a bond is broken); e.g. see the "bond_style
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quartic"_bond_style.html command.
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For style {stats} no interactions are turned off (or on); the status
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of all interactions in the specified group is simply reported. This
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is useful for diagnostic purposes if bonds have been turned off by a
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bond-breaking potential during a previous run.
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The default behavior of the delete_bonds command is to turn off
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interactions by toggling their type to a negative value, but not to
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permanently remove the interaction. E.g. a bond_type of 2 is set to
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-2. The neighbor list creation routines will not include such an
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interaction in their interaction lists. The default is also to not
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alter the list of 1-2, 1-3, 1-4 neighbors computed by the
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"special_bonds"_special_bonds.html command and used to weight pairwise
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force and energy calculations. This means that pairwise computations
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will proceed as if the bond (or angle, etc) were still turned on.
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Several keywords can be appended to the argument list to alter the
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default behaviors.
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The {any} keyword changes the requirement that all atoms in the bond
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(angle, etc) must be in the specified group in order to turn-off the
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interaction. Instead, if any of the atoms in the interaction are in
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the specified group, it will be turned off (or on if the {undo}
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keyword is used).
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The {undo} keyword inverts the delete_bonds command so that the
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specified bonds, angles, etc are turned on if they are currently
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turned off. This means a negative value is toggled to positive. For
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example, for style {angle}, if {type} is specified as 2, then all
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angles with current type = -2, are reset to type = 2. Note that the
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"fix shake"_fix_shake.html command also sets bond and angle types
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negative, so this option should not be used on those interactions.
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The {remove} keyword is invoked at the end of the delete_bonds
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operation. It causes turned-off bonds (angles, etc) to be removed
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from each atom's data structure and then adjusts the global bond
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(angle, etc) counts accordingly. Removal is a permanent change;
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removed bonds cannot be turned back on via the {undo} keyword.
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Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list.
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The {special} keyword is invoked at the end of the delete_bonds
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operation, after (optional) removal. It re-computes the pairwise 1-2,
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1-3, 1-4 weighting list. The weighting list computation treats
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turned-off bonds the same as turned-on. Thus, turned-off bonds must
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be removed if you wish to change the weighting list.
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Note that the choice of {remove} and {special} options affects how
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1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that
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have been modified by the delete_bonds command.
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[Restrictions:]
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This command requires inter-processor communication to acquire ghost
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atoms, to coordinate the deleting of bonds, angles, etc between atoms
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shared by multiple processors. This means that your system must be
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ready to perform a simulation before using this command (force fields
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setup, atom masses set, etc). Just as would be needed to run
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dynamics, the force field you define should define a cutoff
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(e.g. through a "pair_style"_pair_style.html command) which is long
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enough for a processor to acquire the ghost atoms its needs to compute
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bond, angle, etc interactions.
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If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
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weighting list is not recomputed, this can cause a later "fix
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shake"_fix_shake.html command to fail due to an atom's bonds being
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inconsistent with the weighting list. This should only happen if the
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group used in the fix command includes both atoms in the bond, in
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which case you probably should be recomputing the weighting list.
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[Related commands:]
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"neigh_modify"_neigh_modify.html exclude,
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"special_bonds"_special_bonds.html, "fix shake"_fix_shake.html
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[Default:] none
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