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discuss that only turning off bonds can lead to "bond atom missing" errors

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also make notes and this warning stand out more by using adminition boxes
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Axel Kohlmeyer
2025-01-18 09:08:08 -05:00
parent efd5165707
commit 7ffe04ca92
1 changed files with 29 additions and 12 deletions
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doc/src/delete_bonds.rst
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@ -62,6 +62,18 @@ 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* if all the atoms involved are in the specified group. See the *any*
keyword to change the behavior. keyword to change the behavior.
.. admonition:: Possible errors caused by using *delete_bonds*
:class: warning
Since this command by default only *turns off* bonded interactions,
their definitions are still present and subject to the limitations
due to LAMMPS' domain decomposition based parallelization. That is,
when a bond is turned off, the two constituent atoms may move apart
and may reach a distance where they can lead to a "bond atoms missing"
error and crash the simulation. Adding the *remove* keyword (see
below) is required to fully remove those interactions and prevent
the error.
Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*, *improper*\ ) Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*, *improper*\ )
take a *type* as an argument. The specified *type* can be a take a *type* as an argument. The specified *type* can be a
:doc:`type label <Howto_type_labels>`. Otherwise, the type should be an :doc:`type label <Howto_type_labels>`. Otherwise, the type should be an
@ -98,6 +110,9 @@ of all interactions in the specified group is simply reported. This
is useful for diagnostic purposes if bonds have been turned off by a is useful for diagnostic purposes if bonds have been turned off by a
bond-breaking potential during a previous run. bond-breaking potential during a previous run.
.. admonition:: Impact on special_bonds processing and exclusions
:class: note
The default behavior of the delete_bonds command is to turn off The default behavior of the delete_bonds command is to turn off
interactions by toggling their type to a negative value, but not to interactions by toggling their type to a negative value, but not to
permanently remove the interaction. For example, a bond_type of 2 is set to permanently remove the interaction. For example, a bond_type of 2 is set to
@ -138,9 +153,11 @@ operation, after (optional) removal. It re-computes the pairwise 1--2,
turned-off bonds the same as turned-on. Thus, turned-off bonds must turned-off bonds the same as turned-on. Thus, turned-off bonds must
be removed if you wish to change the weighting list. be removed if you wish to change the weighting list.
Note that the choice of *remove* and *special* options affects how .. note::
1--2, 1--3, 1--4 pairwise interactions will be computed across bonds that
have been modified by the delete_bonds command. 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 Restrictions
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