bond/react: RMSD constraint docs

discussion of the 'update_edges' keyword. The fifth optional section

begins with the keyword 'Constraints' and lists additional criteria

that must be satisfied in order for the reaction to occur. Currently,

there are four types of constraints available, as discussed below:

'distance', 'angle', 'dihedral', and 'arrhenius'.

there are five types of constraints available, as discussed below:

'distance', 'angle', 'dihedral', 'arrhenius', and 'RMSD'.

A sample map file is given below:

generated using *seed*\ ; if this number is less than the result of the

Arrhenius equation above, the reaction is permitted to occur.

The constraint of type 'RMSD' has the following syntax:

.. parsed-literal::

   RMSD *RMSDmax* *molfragment*

where 'RMSD' is the required keyword, and *RMSDmax* is the maximum

root-mean-square deviation between atom positions of the pre-reaction

template and the local reaction site, after optimal translation and

rotation of the pre-reaction template. Optionally, a molecule fragment

(of the pre-reaction template) can be specified by *molfragment*\ .

Only atoms that are part of this molecule fragment are used to

determine the RMSD. A molecule fragment must have been defined in the

:doc:`molecule <molecule>` command for the pre-reaction template. For

example, the molecule fragment could consist of only the backbone

atoms of a polymer chain. This constraint can be used to enforce a

specific relative position and orientation between reacting molecules.

Once a reaction site has been successfully identified, data structures

within LAMMPS that store bond topology are updated to reflect the

post-reacted molecule template. All force fields with fixed bonds,