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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*
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*\ )
take a *type* as an argument. The specified *type* can be a
:doc:`type label <Howto_type_labels>`. Otherwise, the type should be an
@ -98,15 +110,18 @@ 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. For example, a bond_type of 2 is set to
:math:`-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, or 1--4 neighbors computed by the
:doc:`special_bonds <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.
.. admonition:: Impact on special_bonds processing and exclusions
:class: note
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. For example, a bond_type of 2 is set to
:math:`-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, or 1--4 neighbors computed by the
:doc:`special_bonds <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.
@ -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
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.
.. note::
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
""""""""""""