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The
Worm model is that of a continuous and unbranched
chain. Each link in the chain consists of one atom
which is connected to no more than two other. The
ends of the chain may be joined to form a closed
circle.
The
force field consists of four terms:
Bonds,
Angles,
Torsions
and SoftSphereX.
Bonds are always present. The
Torsions term can be added only if
Angles are also added.
A
chain may be homogeneous: every link in the chain
is made up of the same kind of atom. Or, the chain
may be heterogeneous: the atoms may be of different
types.
Modules
are located within the Yup package at
Yup/Models/Worm/.
The FFA
and Analyzer
modules are designed for public use while the
const
module is not.
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Module
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Summary
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const
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Constants
for the Worm modules: constructor
functions and labels for the force
terms; the location of the parameter
library and a table containing legal
prefixes, atom inclusion types, atom
exclusion types and atomic
masses.
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FFA
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Force
Field Assembler Class and Function to
create and manipulate worm
models.
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Analyzer
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Functions
to analyze Worm models
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The
const
module defines the parameter library as
Yup/Data/Worm/
(within the Yup package). However, the user can
create and use a different library.
In
order to do this, first create a text file called
source-of-constants
in a previously empty directory. See
FPF
for the format of this document or copy it from the
standard parameter library. Do not change the
number of, or the names of, the inclusion and
exclusion atom types. You can only modify existing
interaction types (change the force field
parameters), add new interaction types, or remove
existing interaction types. (An interaction type is
a combination of atom types, for example, a pair of
atom types form a Bonds interaction type. It
is necessary to define interaction types for all
combinations that can occur in a model. At the same
time, it is desirable to omit interaction types for
illogical combinations, e.g., for two atom types
that cannot form a bond.) When
source-of-constants
is ready, run the program Yup.fpf
to convert it to a number of database files. Pass
the path (to the enclosing directory) to the
constructor function Worm().
The
force field assembler is subclassed from the
template Chains
in Yup.Tools.Chains The force field assembler also
make use of the functions in the LinSeq
module which can also be found in
Yup.Tools.
Force
Field Assembly
Analysis
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