Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
L
lammps
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container Registry
Model registry
Operate
Environments
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
multiscale
lammps
Commits
afaaf442
Commit
afaaf442
authored
6 years ago
by
jrgissing
Browse files
Options
Downloads
Patches
Plain Diff
bond/react doc tweaks 2
parent
cf3aee90
No related branches found
Branches containing commit
No related tags found
No related merge requests found
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
doc/src/fix_bond_react.txt
+1
-1
1 addition, 1 deletion
doc/src/fix_bond_react.txt
doc/utils/sphinx-config/false_positives.txt
+1
-0
1 addition, 0 deletions
doc/utils/sphinx-config/false_positives.txt
src/USER-MISC/fix_bond_react.cpp
+2
-2
2 additions, 2 deletions
src/USER-MISC/fix_bond_react.cpp
with
4 additions
and
3 deletions
doc/src/fix_bond_react.txt
+
1
−
1
View file @
afaaf442
...
...
@@ -318,7 +318,7 @@ unwanted by-products. Therefore, bond/react provides the option to
delete a user-specified set of atoms. These pre-reaction atoms are
identified in the map file. A deleted atom must still be included in
the post-reaction molecule template, in which it cannot be bonded to
an
un
deleted
atom
. In addition to deleting unwanted reaction
an
atom that is not
deleted. In addition to deleting unwanted reaction
by-products, this feature can be used to remove specific topologies,
such as small rings, that may be otherwise indistinguishable.
...
...
This diff is collapsed.
Click to expand it.
doc/utils/sphinx-config/false_positives.txt
+
1
−
0
View file @
afaaf442
...
...
@@ -507,6 +507,7 @@ deepskyblue
defgrad
deformable
del
deleteIDs
Dellago
delocalization
delocalized
...
...
This diff is collapsed.
Click to expand it.
src/USER-MISC/fix_bond_react.cpp
+
2
−
2
View file @
afaaf442
...
...
@@ -1653,13 +1653,13 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
}
}
// additionally, if a deleted atom is bonded to a
un
deleted
atom
, bad
// additionally, if a deleted atom is bonded to a
n atom that is not
deleted, bad
for
(
int
i
=
0
;
i
<
onemol
->
natoms
;
i
++
)
{
if
(
delete_atoms
[
i
][
myrxn
]
==
1
)
{
int
ii
=
reverse_equiv
[
i
][
1
][
myrxn
]
-
1
;
for
(
int
j
=
0
;
j
<
twomol_nxspecial
[
ii
][
0
];
j
++
)
{
if
(
delete_atoms
[
equivalences
[
twomol_xspecial
[
ii
][
j
]
-
1
][
1
][
myrxn
]
-
1
][
myrxn
]
==
0
)
{
error
->
one
(
FLERR
,
"A deleted atom cannot
be
bonded to an
un
deleted
atom
"
);
error
->
one
(
FLERR
,
"A deleted atom cannot
remain
bonded to an
atom that is not
deleted"
);
}
}
}
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment