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nbody_Dihedrals.py
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Created
Wed, Jul 17, 08:41
Size
1 KB
Mime Type
text/x-python
Expires
Fri, Jul 19, 08:41 (2 d)
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blob
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Raw Data
Handle
19111769
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rLAMMPS lammps
nbody_Dihedrals.py
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from
nbody_graph_search
import
Ugraph
# To find 4-body "dihedral" interactions, we would use this subgraph:
#
# 1st bond connects atoms 0 and 1
# *---*---*---* => 2nd bond connects atoms 1 and 2
# 0 1 2 3 3rd bond connects atoms 2 and 3
#
bond_pattern
=
Ugraph
([(
0
,
1
),
(
1
,
2
),
(
2
,
3
)])
# (Ugraph atom indices begin at 0, not 1)
def
canonical_order
(
match
):
"""
When searching for atoms with matching bond patterns GraphMatcher
often returns redundant results. We must define a "canonical_order"
function which sorts the atoms and bonds in a way which is consistent
with the type of N-body interaction being considered.
The atoms (and bonds) in a candidate match are rearranged by the
canonical_order(). Then the re-ordered list of atom and bond ids is
tested against the list of atom/bond ids in the matches-found-so-far,
before it is added to the list of interactions found so far.
(For example, it does not make sense to define a separate 4-body dihedral-
angle interaction between atoms 1, 2, 3, 4 AND 4, 3, 2, 1. The dihedral-
angle is not altered when the order of atoms is reversed, so we arbitrarily
choose whichever order causes the first atom to have the lower atomID.)
"""
# match[0][0:3] contains the ID numbers of the 4 atoms in the match
atom0
=
match
[
0
][
0
]
atom1
=
match
[
0
][
1
]
atom2
=
match
[
0
][
2
]
atom3
=
match
[
0
][
3
]
# match[1][0:2] contains the ID numbers of the the 3 bonds
bond0
=
match
[
1
][
0
]
bond1
=
match
[
1
][
1
]
bond2
=
match
[
1
][
2
]
if
atom0
<
atom3
:
#return ((atom0, atom1, atom2, atom3), (bond0, bond1, bond2)) same as:
return
match
else
:
return
((
atom3
,
atom2
,
atom1
,
atom0
),
(
bond2
,
bond1
,
bond0
))
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