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Merge pull request #1517 from jrgissing/bond/react-clarify-template-check-messages

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Bond/react: clarify reaction-template warning messages
This commit is contained in:
Axel Kohlmeyer
2019-06-17 14:14:53 -04:00
committed by GitHub
parent 1452d3d25b 4178c5167b
commit a39a35af20
4 changed files with 36 additions and 29 deletions
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12
doc/src/Errors_messages.txt
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@ -636,12 +636,12 @@ Please ensure reaction map files are properly formatted. :dd
{Bond/react: Atom affected by reaction too close to template edge} :dt
This means an atom which changes type 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. :dd
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. :dd
{Bond/react: Fix bond/react needs ghost atoms from farther away} :dt

10
doc/src/Errors_warnings.txt
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@ -82,10 +82,14 @@ bond/angle/dihedral. LAMMPS computes this by taking the maximum bond
length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch. :dd
{Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type} :dt
{Bond/react: Atom affected by reaction too close to template edge} :dt
You may want to double-check that all atom types are properly assigned
in the post-reaction template. :dd
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. :dd
{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt