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Added documentation regarding global and family-specific forbidden groups.
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documentation/source/users/rmg/database/kinetics.rst

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@@ -162,6 +162,46 @@ Additionally, groups can also be defined as unions of other groups. For example,
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label="X_H_or_Xrad_H",
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group=OR{X_H, Xrad_H},
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Forbidden Groups
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----------------
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Forbidden groups can be defined to ban structures globally in RMG or to
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ban pathways in a specific kinetic family.
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Globally forbidden structures will ban all reactions containing either reactants
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or products that are forbidden. These groups are stored in in the file located at
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``RMG-database/input/forbiddenStructures.py``.
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To ban certain specific pathways in the kinetics
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families, a `forbidden` group must be created, like the following group
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in the ``intra_H_migration`` family ::
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forbidden(
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label = "bridged56_1254",
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group =
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"""""""
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1 *1 C 1 {2,S} {6,S}
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2 *4 C 0 {1,S} {3,S} {7,S}
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3 C 0 {2,S} {4,S}
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4 *2 C 0 {3,S} {5,S} {8,S}
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5 *5 C 0 {4,S} {6,S} {7,S}
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6 C 0 {1,S} {5,S}
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7 C 0 {2,S} {5,S}
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8 *3 H 0 {4,S}
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""",
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shortDesc = u"""""",
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longDesc =
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u"""
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""",
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)
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Forbidden groups should be placed inside the groups.py file located inside the
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specific kinetics family's folder ``RMG-database/input/kinetics/family_name/``
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alongside normal group entries. The starred atoms in the forbidden group
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ban the specified reaction recipe from occurring in matched products and reactants.
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Hierarchical Trees
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------------------

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