|
This
Soft Sphere term is of the Inclusion type (i.e.,
indexed by the Atom Inclusion Type). An Exclusion
version of this term is also available, see
[SoftSphereX]. An individual term
is:
|
{
|
Ks(
rij
-
do
)n
|
, if
rij
<
do
|
|
0
|
, if
rij
>=
do
|
where
rij is the distance between atoms
i and j, Ks is a
force constant, do is the contact
distance and n is a user-specified power. In
contrast to the van der Waals term, the Soft Sphere
term has no attractive component and the repulsion
component operates only when two atoms are closer
together than their contact distance. The repulsion
component is also much softer than in the van der
Waals term although the user may adjust the
softness by specifying larger values of n.
This is a single value specified for the whole
module (and therefore applied equally to all
pairs). It must be a whole number and the value
must be at least 2.
The
SoftSphereI
module is located in the Energy sub-directory of
the Yup package, hence:
Yup.Energy.SoftSphereI.
The
soft sphere term is introduced into a simulation by
first creating an (empty) instance of the
SoftSphereI
object. Participating atom pairs are then added to
this object. Previously added pairs may also be
deleted or modified. All these actions affect only
a list of candidate pairs. The compile process
binds Coordinate and Gradient
AtomVectors
to the SoftSphereI
module and then goes through the candidate pairs to
form a compiled pair list in which all the atoms
that are involved and the soft sphere parameters
that they are to use are positively identified.
Only then can the soft sphere term be evaluated.
(Prior attempts at evaluation will either yield an
exception or null results.) The evaluate method
would now be called many times as part of a
molecular mechanics calculation. Each call would
yield different results even though the compiled
pair list is fixed because the Coordinates are
different at each call. However, it is possible to
modify the soft sphere parameters
(Ks and do)
continuously during a calculation. The parameters
are accessed through the subscript operator. More
radical changes can be made by adding new pairs and
modifying or deleting existing pairs. These actions
affect the candidate list and immediately clear the
compiled list. Therefore the
SoftSphereI
module must be compiled again before evaluation can
resume. The state of the
SoftSphereI
module can be judged by examining the data
attributes. The compiled pairs can also be examined
in great detail by printing the object.
This
manual is divided into several pages:
|
Name
|
Content
|
|
SoftSphereI
|
Introduction:
this page.
|
|
Create
|
Creating
a new SoftSphereI
object. The function
SoftSphereI().
|
|
Data
|
The
data attributes of a
SoftSphereI
object; some of which may be assigned
new values.
|
|
Manage
|
Managing
soft sphere pairs: add new pairs,
modifying existing pairs and deleting
existing pairs. The methods:
add(),
modify()
and delete().
|
|
Compile
|
Preparing
a SoftSphereI
object for evaluation of the energy and
gradients. The methods:
update()
and compile().
|
|
Evaluate
|
Evaluate
the soft sphere energy and gradients.
The method:
evaluate().
|
|
Subscript
|
The
subscript []
operator: used to access and to assign
values to the soft sphere
parameters
|
|
Print
|
Documents
the print, repr, delete and compare
operators.
|
|
Write
|
Writing
the finalized soft sphere record to the
force field file.
|
|