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update broken bond doc page

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Steve Plimpton
2023-05-01 15:17:19 -06:00
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doc/src/Howto_broken_bonds.rst
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Broken Bonds
============
Typically, bond interactions persist for the duration of a simulation in
LAMMPS. However, there are some exceptions that allow for bonds to
break, including the :doc:`quartic bond style <bond_quartic>` and the
bond styles in the :doc:`BPM package <Howto_bpm>` which contains the
:doc:`bpm/spring <bond_bpm_spring>` and :doc:`bpm/rotational
<bond_bpm_rotational>` bond styles. In these cases, a bond can be broken
if it is stretched beyond a user-defined threshold. LAMMPS accomplishes
this by setting the bond type to 0, such that the bond force is no
longer computed.
Typically, bond interactions persist for the duration of a simulation
in LAMMPS. However, some commands allow bonds to break, including the
following:
Users are normally able to weight the contribution of pair forces to atoms
that are bonded using the :doc:`special_bonds command <special_bonds>`.
When bonds break, this is not always the case. For the quartic bond style,
pair forces are always turned off between bonded particles. LAMMPS does
this via a computational sleight-of-hand. It subtracts the pairwise
interaction as part of the bond computation. When the bond breaks, the
subtraction stops. For this to work, the pairwise interaction must always
be computed by the :doc:`pair_style <pair_style>` command, whether the bond
is broken or not. This means that :doc:`special_bonds <special_bonds>` must
be set to 1,1,1. After the bond breaks, the pairwise interaction between the
two atoms is turned on, since they are no longer bonded.
* :doc:`bond_style quartic <bond_quartic>`
* :doc:`fix bond/break <fix_bond_break>`
* :doc:`fix bond/react <fix_bond_react>`
* :doc:`BPM package <Howto_bpm>` bond styles
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.
A bond can break if it is stretched beyond a user-defined threshold or
more generally if other criteria are met.
Bonds can also be broken by fixes which change bond topology, including
:doc:`fix bond/break <fix_bond_break>` and
:doc:`fix bond/react <fix_bond_react>`. These fixes will automatically
trigger a rebuild of the neighbor list and update special bond data structures
when bonds are broken.
For the quartic bond style, when a bond is broken its bond type is set
to 0 and pairwise forces between the two atoms in the broken bond are
"turned on". Angles, dihedrals, etc cannot be defined for the system
when :doc:`bond_style quartic <bond_quartic>` is used.
Note that when bonds are dumped to a file via the :doc:`dump local <dump>` command, bonds with type 0 are not included. The
:doc:`delete_bonds <delete_bonds>` command can also be used to query the
status of broken bonds or permanently delete them, e.g.:
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 also defines angles, dihedrals, etc. These fixes will
update internal topology data structures when bonds are broken, so
that the appropriate angle, dihederal, etc interactions are also
turned off. They will 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.
The :doc:`delete_bonds <delete_bonds>` command can also be used to
query the status of broken bonds (type = 0) or permanently delete
them, e.g.:
.. code-block:: LAMMPS
delete_bonds all stats
delete_bonds all bond 0 remove
The compute :doc:`nbond/atom <compute_nbond_atom>` can also be used
to tally the current number of bonds per atom, excluding broken bonds.
The compute :doc:`count/type bond <compute_count_type>` command
tallies the current number of bonds for each bond type. It also
tallies broken bonds with type = 0.
The compute :doc:`nbond/atom <compute_nbond_atom>` command tallies the
current number of bonds each atom is part of, excluding broken bonds
with type = 0.