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< title > delete_bonds command — LAMMPS documentation< / title >
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< span id = "index-0" > < / span > < h1 > delete_bonds command< a class = "headerlink" href = "#delete-bonds-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > delete_bonds group-ID style arg keyword ...
< / pre > < / div >
< / div >
< ul >
< li > < p class = "first" > group-ID = group ID< / p >
< / li >
< li > < dl class = "first docutils" >
< dt > style = < em > multi< / em > or < em > atom< / em > or < em > bond< / em > or < em > angle< / em > or < em > dihedral< / em > or< / dt >
< dd > < p class = "first last" > < em > improper< / em > or < em > stats< / em > < / p >
< / dd >
< / dl >
< / li >
< / ul >
< pre class = "literal-block" >
< em > multi< / em > arg = none
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< em > atom< / em > arg = an atom type or range of types (see below)
< em > bond< / em > arg = a bond type or range of types (see below)
< em > angle< / em > arg = an angle type or range of types (see below)
< em > dihedral< / em > arg = a dihedral type or range of types (see below)
< em > improper< / em > arg = an improper type or range of types (see below)
< em > stats< / em > arg = none
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< / pre >
< ul class = "simple" >
< li > zero or more keywords may be appended< / li >
< li > keyword = < em > any< / em > or < em > undo< / em > or < em > remove< / em > or < em > special< / em > < / li >
< / ul >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > 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 > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Turn off (or on) molecular topology interactions, i.e. bonds, angles,
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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
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off via the < a class = "reference internal" href = "neigh_modify.html" > < em > neigh_modify exclude< / em > < / a > command. The
< a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > command also effectively turns off certain
bond and angle interactions.< / p >
< p > 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 < em > any< / em >
keyword to change the behavior.< / p >
< p > Several of the styles (< em > atom< / em > , < em > bond< / em > , < em > angle< / em > , < em > dihedral< / em > ,
< em > improper< / em > ) take a < em > type< / em > as an argument. The specified < em > type< / em > should
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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
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style < em > bond< / em > ; see details below. In all cases, a wildcard asterisk
can be used in place of or in conjunction with the < em > type< / em > argument to
specify a range of types. This takes the form “ *” or “ < em > n” or “ n< / em > ” or
“ 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
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
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non-bond styles; it will simply be ignored.< / p >
< p > For style < em > multi< / em > all bond, angle, dihedral, and improper interactions
of any type, involving atoms in the group, are turned off.< / p >
< p > Style < em > atom< / em > is the same as style < em > multi< / em > 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.< / p >
< p > For style < em > bond< / em > , only bonds are candidates for turn-off, and the bond
must also be of the specified type. Styles < em > angle< / em > , < em > dihedral< / em > , and
< em > improper< / em > are treated similarly.< / p >
< p > For style < em > bond< / em > , 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 < a class = "reference internal" href = "bond_style.html" > < em > bond_style quartic< / em > < / a > command.< / p >
< p > For style < em > stats< / em > no interactions are turned off (or on); the status
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of all interactions in the specified group is simply reported. This
is useful for diagnostic purposes if bonds have been turned off by a
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bond-breaking potential during a previous run.< / p >
< p > 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
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
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< a class = "reference internal" href = "special_bonds.html" > < em > special_bonds< / em > < / a > 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.< / p >
< p > Several keywords can be appended to the argument list to alter the
default behaviors.< / p >
< p > The < em > any< / em > 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 < em > undo< / em >
keyword is used).< / p >
< p > The < em > undo< / em > 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 < em > angle< / em > , if < em > type< / em > 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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< a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > command also sets bond and angle types
negative, so this option should not be used on those interactions.< / p >
< p > The < em > remove< / em > 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 < em > undo< / em > keyword.
Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list.< / p >
< p > The < em > special< / em > 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,
1-3, 1-4 weighting list. The weighting list computation treats
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.< / p >
< p > Note that the choice of < em > remove< / em > and < em > special< / em > 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.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
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< p > 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 < a class = "reference internal" href = "pair_style.html" > < em > pair_style< / em > < / a > command) which is long
enough for a processor to acquire the ghost atoms its needs to compute
bond, angle, etc interactions.< / p >
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< p > If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
weighting list is not recomputed, this can cause a later < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > 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
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.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "neigh_modify.html" > < em > neigh_modify< / em > < / a > exclude,
< a class = "reference internal" href = "special_bonds.html" > < em > special_bonds< / em > < / a > , < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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