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nbody_Impropers_Jcenter.py
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Sat, Sep 7, 19:23
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text/x-python
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Mon, Sep 9, 19:23 (2 d)
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rLAMMPS lammps
nbody_Impropers_Jcenter.py
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from
nbody_graph_search
import
Ugraph
# To find 4-body "improper" interactions,
# (by default, most of the time), we would use this subgraph:
# 0
# * 1st bond connects atoms 1 and 0
# | => 2nd bond connects atoms 1 and 2
# _.*._ 3rd bond connects atoms 1 and 3
# *' 1 `*
# 2 3
#
# In OPLS, the central atom is the second atom ("1").
# This differs from other force-fields.
# We take this detail into account in the line below:
bond_pattern
=
Ugraph
([(
1
,
0
),
(
1
,
2
),
(
1
,
3
)])
# As with other force-fields, the improper-angle is the angle between the planes
# defined by the first three atoms (0,1,2) and last three atoms (1,2,3).
# (This is implemented in LAMMPS using an improper_style which requires
# that the atoms in the interaction will be listed in this order: 0,1,2,3.)
def
canonical_order
(
match
):
"""
Before defining a new interaction, we must check to see if an
interaction between these same 4 atoms has already been created
(perhaps listed in a different, but equivalent order).
If we don't check for this this, we will create many unnecessary redundant
interactions (which can slow down he simulation).
To avoid this, I define a "canonical_order" function which sorts the atoms
and bonds in a way which is consistent with the symmetry of the interaction
being generated... Later the re-ordered list of atom and bond ids will be
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. Note that
the energy of an improper interactions is a function of the improper angle.
The improper-angle is usually defined as the angle between planes formed
by atoms 0,1,2 & 1,2,3. (Alternately, it is sometimes defined as the
angle between the 0,1,2 plane and atom 3.)
This angle does not change when swapping the OUTER pair of atoms (0 and 3)
(except for a change of sign, which does not matter since the energy functions
used are typically sign invariant. Furthermore, neither of OUTER pair of atoms
are the central atom. There are 3!=6 ways of ordering the remaining 3 atoms.)
Consequently it does not make sense to define a separate 4-body improper-
interaction between atoms 0,1,2,3 AS WELL AS between 3,1,2,0.
So we sort the atoms and bonds so that the first atom has a always has
a lower atomID than the last atom. (Later we will check to see if we
have already defined an interaction between these 4 atoms. If not then
we create a new one.)
"""
atom0
=
match
[
0
][
0
]
atom1
=
match
[
0
][
1
]
atom2
=
match
[
0
][
2
]
atom3
=
match
[
0
][
3
]
# match[1][0:2] contains the ID numbers for 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))
# But this is the same thing as:
return
match
else
:
return
((
atom3
,
atom1
,
atom2
,
atom0
),
(
bond2
,
bond1
,
bond0
))
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