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nbody_Dihedrals_nosym.py
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Thu, Sep 12, 23:01
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rLAMMPS lammps
nbody_Dihedrals_nosym.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.
However, some dihedral_styles (such as dihedral_style class2)
have no symmetry (at least not for arbitrary choices of parameters).
These force-field styles, the different permulations of atom-order
are not equivalent. So we do not want to rearrange the order of
the atoms (and bonds) in the match, because the formula for the
interaction between atoms 1,2,3,4 is not the same as the formula
for the interaction between atoms 4,3,2,1.
In this case, this function returns
the original "match" argument unmodified.
"""
return
match
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