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