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Clarifying how BPM package works

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This commit is contained in:
Joel Thomas Clemmer
2023-05-02 14:28:17 -06:00
parent 6d050374c3
commit 36632e3356
2 changed files with 16 additions and 12 deletions
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14
doc/src/Howto_broken_bonds.rst
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@ -19,6 +19,14 @@ in the broken bond are "turned on". Angles, dihedrals, etc cannot be
defined for a system when :doc:`bond_style quartic <bond_quartic>` is
used.
Similarly, bond styles in the BPM package are also incompatible with
angles, dihedrals, etc. and when a bond breaks its type is set to zero.
However, in the BPM package one can either turn off all pair interactions
between bonded particles or leave them on, overlaying pair forces on
top of bond forces. To remove pair forces, the special bond list is
dynamically updated. More details can be found on the :doc:`Howto BPM
<Howto_bpm>` page.
The :doc:`fix bond/break <fix_bond_break>` and :doc:`fix bond/react
<fix_bond_react>` commands allow breaking of bonds within a molecular
topology with may also define angles, dihedrals, etc. These commands
@ -27,12 +35,6 @@ well as the appropriate angle, dihederal, etc interactions which
include the bond. They also trigger a rebuild of the neighbor list
when this occurs, to turn on the appropriate pairwise forces.
In the BPM package, one can either turn off all pair interactions
between bonded particles or leave them on, overlaying pair forces on
top of bond forces. To remove pair forces, the special bond list is
dynamically updated. More details can be found on the :doc:`Howto BPM
<Howto_bpm>` page.
Note that when bonds are dumped to a file via the :doc:`dump local
<dump>` command, bonds with type 0 are not included.

14
doc/src/compute_count_type.rst
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@ -54,8 +54,9 @@ type:
These commands can create and/or break topological bonds (angles,
etc). In the case of breaking, they remove the bond (angle, etc) from
the system, so that they no longer exist (:doc:`bond_style quartic
<bond_quartic>` is the exception, see the discussion below). Thus
they are not included in the counts for each type:
<bond_quartic>` and :doc:`BPM bond styles <Howto_bpm>` are exceptions,
see the discussion below). Thus they are not included in the counts
for each type:
* :doc:`delete_bonds remove <delete_bonds>`
* :doc:`bond_style quartic <bond_quartic>`
@ -74,10 +75,11 @@ type is tallied. Only bonds with both atoms in the specified group
are counted.
For {mode} = {bond}, broken bonds with a bond type of zero are also
counted. The :doc:`bond_style quartic <bond_quartic>` breaks a bond
by doing this. See the :doc:`Howto broken bonds <Howto_broken_bonds>`
doc page for more details. Note that the group setting is ignored for
broken bonds; all broken bonds in the system are counted.
counted. The :doc:`bond_style quartic <bond_quartic>` and :doc:`BPM
bond styles <Howto_bpm>` break bonds by doing this. See the :doc:`
Howto broken bonds <Howto_broken_bonds>` doc page for more details.
Note that the group setting is ignored for broken bonds; all broken
bonds in the system are counted.
If the {mode} setting is {angle} then the count of angles for each
angle type is tallied. Only angles with all 3 atoms in the specified