diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index e03c4b3ac7..e6825ded33 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -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 `. 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 ` 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 ` 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 """"""""""""