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bond/react doc final touches

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jrgissing 2019-06-02 12:35:38 -06:00
parent 58a88dff95
commit 983f3adbb4
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doc/src/fix_bond_react.txt
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@ -18,8 +18,8 @@ fix ID group-ID bond/react common_keyword values ...
ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
bond/react = style name of this fix command :l
zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
these apply to all reaction specifications (below) :l
the common keyword/values may be appended directly after 'bond/react' :l
this applies to all reaction specifications (below) :l
common_keyword = {stabilization} :l
{stabilization} values = {no} or {yes} {group-ID} {xmax}
{no} = no reaction site stabilization
@ -309,26 +309,25 @@ can allow for the possibility of one or more reverse reactions.
The optional keywords deal with the probability of a given reaction
occurring as well as the stable equilibration of each reaction site as
it occurs.
it occurs:
The {prob} keyword can affect whether an eligible reaction actually
occurs. The fraction setting must be a value between 0.0 and 1.0. A
uniform random number between 0.0 and 1.0 is generated and the
The {prob} keyword can affect whether or not an eligible reaction
actually occurs. The fraction setting must be a value between 0.0 and
1.0. A uniform random number between 0.0 and 1.0 is generated and the
eligible reaction only occurs if the random number is less than the
fraction. Up to N reactions are permitted to occur, as optionally
specified by the {max_rxn} keyword.
The {stabilize_steps} keyword allows for the specification of how many
timesteps a reaction site is stabilized before being returned to the
overall system thermostat.
In order to produce the most physical behavior, this 'reaction site
equilibration time' should be tuned to be as small as possible while
retaining stability for a given system or reaction step. After a
limited number of case studies, this number has been set to a default
of 60 timesteps. Ideally, it should be individually tuned for each fix
reaction step. Note that in some situations, decreasing rather than
increasing this parameter will result in an increase in stability.
overall system thermostat. In order to produce the most physical
behavior, this 'reaction site equilibration time' should be tuned to
be as small as possible while retaining stability for a given system
or reaction step. After a limited number of case studies, this number
has been set to a default of 60 timesteps. Ideally, it should be
individually tuned for each fix reaction step. Note that in some
situations, decreasing rather than increasing this parameter will
result in an increase in stability.
The {update_edges} keyword can increase the number of atoms whose
atomic charges are updated, when the pre-reaction template contains
@ -336,11 +335,11 @@ edge atoms. When the value is set to 'charges,' all atoms' atomic
charges are updated to those specified by the post-reaction template,
including atoms near the edge of reaction templates. When the value is
set to 'custom,' an additional section must be included in the map
file that specifies whether to update charges, on a per-atom basis.
The format of this section is detailed above. Listing a pre-reaction
atom ID with a value of 'charges' will force the update of the atom's
charge, even if it is near a template edge. Atoms not near a template
edge are unaffected by this setting.
file that specifies whether or not to update charges, on a per-atom
basis. The format of this section is detailed above. Listing a
pre-reaction atom ID with a value of 'charges' will force the update
of the atom's charge, even if it is near a template edge. Atoms not
near a template edge are unaffected by this setting.
A few other considerations: