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nbody_Impropers.py
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Mon, Jul 8, 19:28

nbody_Impropers.py
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from nbody_graph_search import Ugraph
# This file defines how improper interactions are generated by moltemplate.sh
# by default. It can be overridden by supplying your own custom file
# (for example, see "opls_imp.py")
# To find 4-body "improper" interactions,
# (by default, most of the time), we would use this subgraph:
# 3
# * 1st bond connects atoms 0 and 1
# | => 2nd bond connects atoms 0 and 2
# _.*._ 3rd bond connects atoms 0 and 3
# *' 0 `*
# 1 2
#
bond_pattern = Ugraph([(0,1), (0,2), (0,3)])
# (Ugraph atom indices begin at 0, not 1)
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 MIDDLE pair of atoms (1 and 2)
(except for a change of sign, which does not matter since the energy functions
used are typically sign invariant. Furthermore, neither of MIDDLE pair of atoms
are the central atom, and 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 0,2,1,3.
So we sort the atoms and bonds so that the second atom has a always has
a lower atomID than the third 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 atom1 <= atom2:
#return ((atom0,atom1,atom2,atom3), (bond0,bond1,bond2))
# But this is the same thing as:
return match
else:
return ((atom0,atom2,atom1,atom3), (bond1,bond0,bond2))

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