Interaction Parameters
In the context of gmak, force-field parameters are represented as
interaction-parameter objects. An interaction parameter is initialized
from a string (its name) that may identify the type of the
interaction in the context of the force-field and also the particles
involved. The name of the interaction parameter is also used to
unambiguously associate it to one of the
parameter-search-grid axes.
The value of the interaction parameter is set based on this
association for each grid point.
The following interaction-parameter types are available in gmak.
See also
InteractionParameterThe class of the interaction-parameter object.
Lennard-Jones parameters
Atomtype Parameters
Atomtype parameters are identified by a name with pattern
PARAMETER_ATOMTYPE, where ATOMTYPE is a string identifying the
type of the atom within the forcefield, and PARAMETER is either
the character V or the character W.
If the Lennard-Jones potential is represented in the
\(C_6\)-\(C_{12}\) form, V is interpreted as \(C_6\)
and W, as \(C_{12}\). If it is in the
\(\sigma\)-\(\epsilon\) form, V is interpreted as
\(\sigma\), and W, as \(\epsilon\).
The value of an atomtype parameter directly affects that of the interaction between self pairs, i.e. those involving two atoms of the given atomtype. The effect over standard (i.e., non-1,4) interaction pairs involving one atom of the given atomtype (referred to as the reference atomtype) and a second atom of a different atomtype (referred to as the other atomtype) is controlled by two regular expressions:
- pairs_include
The regular expression controlling which standard pairtypes may have parameters affected by those of the reference atomtype. The regular expression itself matches with the name of the other atomtype. The default value is
.*(matches other atomtypes with any name).- pairs_exclude
The regular expression controlling which standard pairtypes do not have their parameters affected by those of the reference atomtype. The regular expression itself matches with the name of the other atomtype. The default value is
^$(matches nothing).
Only the standard pairtypes that match against the regular expression
pairs_include but not against pairs_exclude are affected by
the reference atomtype.
See also
LJ_V,LJ_WMembers of the enumeration
InteractionParameterTypethat identify standard Lennard-Jones parameters ingmak.
See also
InteractionAtomThe class representing interaction atoms.
See also
derives_from_atom()Method of the
InteractionPairclass used to verify if a pair derives from an atom following the regular-expression rules described above.
Standard-pairtype Parameters
Standard-pairtype parameters are identified by a name with pattern
PARAMETER_ATOMTYPEI_ATOMTYPEJ, where ATOMTYPEI and
ATOMTYPEJ are strings identifying the types of the atoms involved
in the interaction within the force field, and PARAMETER is either
the character V or the character W, as described above.
See also
LJ_V,LJ_WMembers of the enumeration
InteractionParameterTypethat identify standard Lennard-Jones parameters ingmak.
See also
InteractionPairThe class representing interaction pairs.
1,4-pairtype Parameters
1,4-pairtype parameters are identified by a name with pattern
14_PARAMETER_ATOMTYPEI_ATOMTYPEJ, where ATOMTYPEI and
ATOMTYPEJ are strings identifying the types of the atoms involved
in the interaction within the force field, and PARAMETER is either
the character V or the character W, as described above.
The 1,4-pairtype parameters differ from the standard-pairtype parameters in that they are applied exclusively to particles in the same molecule and separated by exactly three consecutive bonds.
See also
LJ_14_V,LJ_14_WMembers of the enumeration
InteractionParameterTypethat identify 1,4 Lennard-Jones parameters ingmak.
See also
InteractionPairThe class representing interaction pairs.
Macro-based parameters
Macro-based parameters are identified by a name that starts with the
@ character.
See also
MacroParameterMember of the enumeration
InteractionParameterTypethat identifies macro-based parameters ingmak.
Custom parameters
Custom parameters are those whose name does not match any of the patterns above. They are an umbrella type to accomodate parameters that are not processed in any special way by the program, leaving this job to the user.
See also
CustomParameterMember of the enumeration
InteractionParameterTypethat identifies custom parameters ingmak.