From 983f3adbb4fe56a55a6f454899286547feb5b338 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sun, 2 Jun 2019 12:35:38 -0600 Subject: [PATCH] bond/react doc final touches --- doc/src/fix_bond_react.txt | 39 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 20 deletions(-) diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 08b0caf282..34f0e6daf7 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -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: