class2_imp.py
No OneTemporary
Actions

Subscribers

None

File Metadata

	from nbody_graph_search import Ugraph

	# This file defines how improper interactions are generated in class2 files.
	# To use it, add "(class2_imp.py)" to the name of the "Data Impropers By Type"
	# section, and make sure this file is located in the "common" directory.
	# For example:
	# write_once("Data Impropers By Type (class2_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):
	"""
	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 improper_styles (such as improper_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 resulting interaction
	is not equivalent. In this case, this function returns
	the original "match" argument unmodified.

	"""

	return match