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add option to update all atoms' atomic charges

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option to update all atomic charges, even when edge atoms are defined
This commit is contained in:
jrgissing
2018-10-30 22:11:52 -06:00
parent e992bf935b
commit 3faecc4d28
3 changed files with 33 additions and 5 deletions
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25
doc/src/fix_bond_react.txt
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@ -41,7 +41,10 @@ react = mandatory argument indicating new reaction specification :l
fraction = initiate reaction with this probability if otherwise eligible
seed = random number seed (positive integer)
{stabilize_steps} value = timesteps
timesteps = number of timesteps to apply internally created nve/limit.html :pre
timesteps = number of timesteps to apply internally created nve/limit.html
{update_edges} value = {none} or {charges} :l
none = do not update topology near the edges of reaction templates
charges = update atomic charges of all atoms in reaction templates :pre
:ule
[Examples:]
@ -155,7 +158,17 @@ Some atoms in the pre-reacted template that are not reacting may have
missing topology with respect to the simulation. For example, the
pre-reacted template may contain an atom that would connect to the
rest of a long polymer chain. These are referred to as edge atoms, and
are also specified in the map file.
are also specified in the map file. When the pre-reaction template
contains edge atoms, not all atoms, bonds, charges, etc. specified in
the reaction templates will be updated. Specifically, topology that
involves only atoms that are 'too near' to template edges will not be
updated. The definition of 'too near the edge' depends on which
interactions are defined in the simulation. If the simulation has
defined dihedrals, atoms within two bonds of edge atoms are considered
'too near the edge.' If the simulation defines angles, but not
dihedrals, atoms within one bond of edge atoms are considered 'too
near the edge.' If just bonds are defined, only edge atoms are
considered 'too near the edge.'
Note that some care must be taken when a building a molecule template
for a given simulation. All atom types in the pre-reacted template
@ -255,6 +268,12 @@ 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.
The {update_edges} keyword can increase the number of atoms whose
atomic charges are updated, when the pre-reaction template contains
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.
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
@ -323,7 +342,7 @@ bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
[Default:]
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none
:line