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document type label support for Shake Bond Types

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This commit is contained in:
Axel Kohlmeyer
2022-09-06 23:27:03 -04:00
parent 0dc3bccb95
commit cfcd5a625d
1 changed files with 15 additions and 10 deletions
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doc/src/molecule.rst
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@ -470,11 +470,15 @@ This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file.
The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c values identically.
The a,b,c values are bond types for all bonds in the SHAKE cluster that
this atom belongs to. Bond types may be either numbers (from 1 to Nbondtypes)
or bond type labels as defined by the :doc:`labelmap <labelmap>` command
or a "Bond Type Labels" section of a data file.
The number of values that must appear is determined by the shake flag
for the atom (see the Shake Flags section above). All atoms in a
particular cluster should list their a,b,c values identically.
If flag = 0, no a,b,c values are listed on the line, just the
(ignored) ID.
@ -482,8 +486,9 @@ If flag = 0, no a,b,c values are listed on the line, just the
If flag = 1, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the second non-central atom (value c in the Shake Atoms section), and c =
the angle type (1 to Nangletypes) of the angle between the 3 atoms.
the second non-central atom (value c in the Shake Atoms section), and c
= the angle type (1 to Nangletypes, or angle type label) of the angle
between the 3 atoms.
If flag = 2, only a is listed, where a = bondtype of the bond between
the 2 atoms in the cluster.
@ -496,9 +501,9 @@ and the second non-central atom (value c in the Shake Atoms section).
If flag = 4, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the second non-central atom (value c in the Shake Atoms section), and c =
bondtype of the bond between the central atom and the third non-central
atom (value d in the Shake Atoms section).
the second non-central atom (value c in the Shake Atoms section), and c
= bondtype of the bond between the central atom and the third
non-central atom (value d in the Shake Atoms section).
See the :doc:`fix shake <fix_shake>` page for a further description
of SHAKE clusters.