diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index fc260de324..453b31e12f 100755 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -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 ` -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 ` 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 ` +command for the pre-reaction template. The constraint of type 'arrhenius' imposes an additional reaction probability according to the temperature-dependent Arrhenius equation: