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Merge pull request #1215 from jrgissing/bond/react-doc-corrections,mostly-formatting

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Bond/react doc corrections,mostly formatting
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Axel Kohlmeyer
2018-11-20 10:50:55 -05:00
committed by GitHub
parent 719f719496 1d4e1f1425
commit d359beb170
1 changed files with 19 additions and 18 deletions
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37
doc/src/fix_bond_react.txt
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@ -25,7 +25,7 @@ common_keyword = {stabilization} :l
{no} = no reaction site stabilization {no} = no reaction site stabilization
{yes} = perform reaction site stabilization {yes} = perform reaction site stabilization
{group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms
{xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre {xmax} = xmax value that is used by an internally-created "nve/limit"_fix_nve_limit.html integrator :pre
react = mandatory argument indicating new reaction specification :l react = mandatory argument indicating new reaction specification :l
react-ID = user-assigned name for the reaction :l react-ID = user-assigned name for the reaction :l
react-group-ID = only atoms in this group are considered for the reaction :l react-group-ID = only atoms in this group are considered for the reaction :l
@ -36,13 +36,13 @@ react = mandatory argument indicating new reaction specification :l
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
zero or more individual keyword/value pairs may be appended to each react argument :l zero or more individual keyword/value pairs may be appended to each react argument :l
individual_keyword = {prob} or {stabilize_steps} :l individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l
{prob} values = fraction seed {prob} values = fraction seed
fraction = initiate reaction with this probability if otherwise eligible fraction = initiate reaction with this probability if otherwise eligible
seed = random number seed (positive integer) seed = random number seed (positive integer)
{stabilize_steps} value = timesteps {stabilize_steps} value = timesteps
timesteps = number of timesteps to apply internally created nve/limit fix :pre timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms
{update_edges} value = {none} or {charges} :l {update_edges} value = {none} or {charges} or {custom}
none = do not update topology near the edges of reaction templates none = do not update topology near the edges of reaction templates
charges = update atomic charges of all atoms in reaction templates charges = update atomic charges of all atoms in reaction templates
custom = force the update of user-specified atomic charges :pre custom = force the update of user-specified atomic charges :pre
@ -95,7 +95,7 @@ necessary because the 'common keywords' are applied to all reactions.
The {stabilization} keyword enables reaction site stabilization. The {stabilization} keyword enables reaction site stabilization.
Reaction site stabilization is performed by including reacting atoms Reaction site stabilization is performed by including reacting atoms
in an internally created fix "nve/limit"_fix_nve_limit.html time in an internally-created fix "nve/limit"_fix_nve_limit.html time
integrator for a set number of timesteps given by the integrator for a set number of timesteps given by the
{stabilize_steps} keyword. While reacting atoms are being time {stabilize_steps} keyword. While reacting atoms are being time
integrated by the internal nve/limit, they are prevented from being integrated by the internal nve/limit, they are prevented from being
@ -122,12 +122,13 @@ due to the internal dynamic grouping performed by fix bond/react.
NOTE: If the group-ID is an existing static group, react-group-IDs NOTE: If the group-ID is an existing static group, react-group-IDs
should also be specified as this static group, or a subset. should also be specified as this static group, or a subset.
NOTE: If the group-ID is previously unused, the internally created NOTE: If the group-ID is previously unused, the internally-created
group applies to all atoms in the system, i.e. you should generally group applies to all atoms in the system, i.e. you should generally
not have a separate thermostat which acts on the 'all' group, or any not have a separate thermostat which acts on the 'all' group, or any
other group. other group.
The following comments pertain to each {react} argument: The following comments pertain to each {react} argument (in other
words, can be customized for each reaction, or reaction step):
A check for possible new reaction sites is performed every {Nevery} A check for possible new reaction sites is performed every {Nevery}
timesteps. timesteps.
@ -202,9 +203,9 @@ A discussion of correctly handling this is also provided on the
The map file is a text document with the following format: The map file is a text document with the following format:
A map file has a header and a body. The header of map file the A map file has a header and a body. The header of map file the
contains one mandatory keyword and two optional keywords. The mandatory contains one mandatory keyword and two optional keywords. The
keyword is 'equivalences' and the optional keywords are 'edgeIDs' and mandatory keyword is 'equivalences' and the optional keywords are
'customIDs': 'edgeIDs' and 'customIDs':
N {equivalences} = # of atoms N in the reaction molecule templates N {equivalences} = # of atoms N in the reaction molecule templates
N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
@ -286,6 +287,14 @@ The {stabilize_steps} keyword allows for the specification of how many
timesteps a reaction site is stabilized before being returned to the timesteps a reaction site is stabilized before being returned to the
overall system thermostat. 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 The {update_edges} keyword can increase the number of atoms whose
atomic charges are updated, when the pre-reaction template contains atomic charges are updated, when the pre-reaction template contains
edge atoms. When the value is set to 'charges,' all atoms' atomic edge atoms. When the value is set to 'charges,' all atoms' atomic
@ -298,14 +307,6 @@ 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 charge, even if it is near a template edge. Atoms not near a template
edge are unaffected by this setting. edge are unaffected by this setting.
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.
A few other considerations: A few other considerations:
It may be beneficial to ensure reacting atoms are at a certain It may be beneficial to ensure reacting atoms are at a certain