jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update fix_bond_react.rst

This commit is contained in:
Jacob Gissinger 2020-05-23 23:12:16 -06:00
parent 4250def29a
commit 60e0a8a6a8
1 changed files with 27 additions and 17 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

44
doc/src/fix_bond_react.rst
View File

@ -300,7 +300,8 @@ either 'none' or 'charges.' Further details are provided in the
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.
there are four types of constraints available, as discussed below:
'distance', 'angle', 'dihedral', and 'arrhenius'.
A sample map file is given below:
@ -353,8 +354,9 @@ has syntax as follows:
distance *ID1* *ID2* *rmin* *rmax*
where 'distance' is the required keyword, *ID1* and *ID2* are
pre-reaction atom IDs, and these two atoms must be separated by a
distance between *rmin* and *rmax* for the reaction to occur.
pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
two atoms must be separated by a distance between *rmin* and *rmax*
for the reaction to occur.
The constraint of type 'angle' has the following syntax:
@ -363,11 +365,11 @@ The constraint of type 'angle' has the following syntax:
angle *ID1* *ID2* *ID3* *amin* *amax*
where 'angle' is the required keyword, *ID1*\ , *ID2* and *ID3* are
pre-reaction atom IDs, and these three atoms must form an angle
between *amin* and *amax* for the reaction to occur (where *ID2* is
the central atom). Angles must be specified in degrees. This
constraint can be used to enforce a certain orientation between
reacting molecules.
pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
three atoms must form an angle between *amin* and *amax* for the
reaction to occur (where *ID2* is the central atom). Angles must be
specified in degrees. This constraint can be used to enforce a certain
orientation between reacting molecules.
The constraint of type 'dihedral' has the following syntax:
@ -376,15 +378,23 @@ The constraint of type 'dihedral' has the following syntax:
dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2*
where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3*
and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in
the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>`
documentation for further details on convention. If *amin* is less
than *amax*, these four atoms must form a dihedral angle greater than
*amin* **and** less than *amax* for the reaction to occur. If *amin*
is greater than *amax*, these four atoms must form a dihedral angle
greater than *amin* **or** less than *amax* for the reaction to occur.
Angles must be specified in degrees. Optionally, a second range of
permissible angles *amin2*-*amax2* can be specified.
and *ID4* are pre-reaction atom IDs (or molecule-fragment IDs, see
below). Dihedral angles are calculated in the interval (-180,180].
Refer to the :doc:`dihedral style <dihedral_style>` documentation for
further details on convention. If *amin* is less than *amax*, these
four atoms must form a dihedral angle greater than *amin* **and** less
than *amax* for the reaction to occur. If *amin* is greater than
*amax*, these four atoms must form a dihedral angle greater than
*amin* **or** less than *amax* for the reaction to occur. Angles must
be specified in degrees. Optionally, a second range of permissible
angles *amin2*-*amax2* can be specified.
For the 'distance', 'angle', and 'dihedral' constraints (explained
above), atom IDs can be replaced by pre-reaction molecule-fragment
IDs. The molecule-fragment ID must begin with a letter. The location
of the ID is the average of all atom positions in the fragment. The
molecule fragment must have been defined in the :doc:`molecule <molecule>`
command for the pre-reaction template.
The constraint of type 'arrhenius' imposes an additional reaction
probability according to the temperature-dependent Arrhenius equation: