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bond/react: docs tweak

This commit is contained in:
jrgissing 2020-02-26 20:08:58 -07:00
parent 9c507e6b81
commit fe1ac99ae7
2 changed files with 10 additions and 11 deletions
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4
doc/src/Errors_messages.rst
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@ -509,14 +509,14 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to superimpose the entire unreacted
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm\_modify cutoff command can be used to extend the communication
range.

17
src/USER-REACTION/fix_bond_react.h
View File

@ -239,18 +239,17 @@ Atom IDs in molecule templates range from 1 to the number of atoms in the templa
E or W: Bond/react: Atom affected by reaction %s too close to template edge
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
reaction is too close to an 'edge' atom defined in the map file. This
could cause incorrect assignment of bonds, angle, etc. Generally, this
means you must include more atoms in your templates, such that there
are at least two atoms between each atom involved in the reaction and
an edge atom.
E: Bond/react: Fix bond/react needs ghost atoms from farther away
This is because a processor needs to superimpose the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
This is because a processor needs to map the entire unreacted molecule
template onto simulation atoms it knows about. The comm_modify cutoff
command can be used to extend the communication range.
E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted