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Each
atom of a molecular model is assigned two mutually
exclusive Atom Types: Inclusion and
Exclusion. The Exclusion Atom Type is
used to index energy terms where all pair
interactions are implied except those that appear
in an Exclusion list.
The
format of the Atom Exclusion Type record
is:
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:ATOM-EXCLUSION-TYPE
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:Name1:
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:Name2:
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...
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:NameN-1:
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:NameN:
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:END
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The
opening and closing keywords, like all keywords,
begin with a colon and start on column one of their
respective lines. The body of the data section
(usually indented for clarity) may contain any
number of lines. A line may be empty or may contain
a name. The name is written between a pair of
colons; the colons are not part of the name.
Following the closing colon may be text to serve as
comment. The comment must be separated from the
name by white space, and may not contain
colons.
An
Atom Exclusion Type name may be as short as
one character and as long as 127 characters. The
name may not include the following three
characters: ":",
"/",
"\".
A name may not be exactly
"^",
"+"
or "-"
but may contain these characters. Names are
case-sensitive. Note that a name may start with
space characters or may even contain only spaces;
such names are useable but may be confusing.
Atom Exclusion and Inclusion Types
are used in different arena so there is no problem
with using the same names for both types but that
may lead to confusion.
There
is no need to arrange the names in any particular
order but the order is significant. The data for
Exclusion list force-field terms must be
supplied in strict order. If there are
N
Atom Exclusion Types there must be
N(N+1)/2
items (lightly shaded cells) in the following
order:
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1
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2
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...
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N-1
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N
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Pair
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:Name1:Name1:
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:Name1:Name2:
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:Name1:...:
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:Name1:NameN-1:
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:Name1:NameN:
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1
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:Name2:Name2:
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:Name2:...:
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:Name2:NameN-1:
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:Name2:NameN:
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2
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:...:...:
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:...:NameN-1:
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:...:NameN:
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...
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:NameN-1:NameN-1:
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:NameN-1:NameN:
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N-1
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:NameN:NameN:
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N
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The
items must be listed across the table then down.
Data for the cross terms must be generated from
data for pure types using mixing rules. The mixing
rules should be documented in the force constants
file. YUP
does not have any hard-coded mixing rules hence the
need to provided data for all pairs. This allows
the user to make use of any mixing rule.
The
program Yup.fpf
will preserve a record of the order of this list,
sort it alphabetically and write this and the
Atom Inclusion Type list to the unformatted
file: "Atom
Exclusion and Inclusion
Types".
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