The mass eigenstates of squarks and sleptons are, in principle,
mixtures of their left- and right-handed components, given by:

where are soft SUSY-breaking parameters for superpartners of doublets, and are parameters for singlets. The -terms associated with Electroweak symmetry breaking are and , where is the weak isospin eigenvalue () of the fermion and is the electric charge. Taking the -terms into account, one easily sees that the masses of sfermions in doublets are related by a sum rule: .

In many high-energy models,
the soft SUSY-breaking sfermion mass parameters are
taken to be equal at the high-energy scale, but, in principle,
they can be different for
each generation or even within a generation.
However, the sfermion flavor dependence can have important effects on
low-energy observables, and it is often strongly constrained.
The suppression of flavor changing neutral currents (FCNC's), such as
, requires that either the squark soft
SUSY-breaking mass matrix is diagonal and degenerate,
or the masses of the
first- and second-generation sfermions are very large. Thus we make the
data-motivated simplification of setting
,
,
,
.

The left-right
sfermion mixing is determined by the product of
soft SUSY-breaking parameters and the mass of
the corresponding fermion.
Unless the soft SUSY-breaking parameters for the first two
generations are orders of magnitude greater than for
the third generation, the mixing in
the first two generations can be neglected. This simplifying assumption is
also made in PYTHIA: the sfermions
, with
,
and
,
with
, are the real mass eigenstates with
masses
and
respectively.
For the third generation sfermions, due to weaker experimental constraints,
the left-right mixing can be nontrivial.
The tree-level
mass matrix for the top squarks (stops) in the (
)
basis is given by

(149) |

where the masses and mixing angle are fixed by diagonalizing the squared-mass matrix Eq. (). Note that different conventions exist also for the mixing angle , and that PYTHIA here agrees with ISASUSY. When translating Feynman rules from the (L,R) to (1,2) basis, we use:

(150) |

Because of the large mixing, the lightest stop can be one of the lightest sparticles. For the sbottom, an analogous formula for the mass matrix holds with , , , , and . For the stau, the substitutions , , , , and 1/ are appropriate. The parameters , , and can be independent, or they might be related by some underlying principle. When or is large ( , left-right mixing can also become relevant for the sbottom and stau.

Most of the SUSY input parameters are needed to specify the
properties of the sfermions. As mentioned earlier, the effects of
mixing between the interaction and mass eigenstates are assumed
negligible for the first two generations. Furthermore, sleptons
and squarks are treated slightly differently. The physical
slepton masses and are set by
`RMSS(6)` and `RMSS(7)`. By default, the
mixing is set by the parameters `RMSS(13)`, `RMSS(14)` and
`RMSS(17)`, which represent , and ,
respectively, i.e. neither -terms nor is included.
However, for `IMSS(8) = 1`, the masses will follow the same
pattern as for the first two generations.
Previously, it was assumed that the soft SUSY-breaking parameters
associated with the stau included -terms. This is no longer the case,
and is more consistent with the treatment of the stop and sbottom.
For the first two generations of squarks,
the parameters `RMSS(8)` and `RMSS(9)` are the mass parameters
and ,
i.e. without -terms included. For more generality, the
choice `IMSS(9) = 1` means that for
is set instead
by `RMSS(22)`, while for is
`RMSS(9)`. Note that the left-handed squark mass parameters
must have the same value since they reside in the same
doublet. For the third generation, the parameters `RMSS(10)`,
`RMSS(11)`, `RMSS(12)`, `RMSS(15)` and `RMSS(16)`
represent , ,
, and , respectively.

There is added
flexibility in the treatment of stops, sbottoms and staus.
With the flag `IMSS(5) = 1`, the properties of the third generation
sparticles can be specified by their mixing angle and mass eigenvalues
(instead of being derived from the soft SUSY-breaking parameters).
The parameters `RMSS(26) - RMSS(28)` specify the mixing angle
(in radians) for the sbottom, stop, and stau. The parameters
`RMSS(10) - RMSS(14)` specify the two stop masses, the one
sbottom mass (the other being fixed by the other parameters) and the
two stau masses. Note that the masses `RMSS(10)` and `RMSS(13)`
correspond to the left-left entries of the diagonalized matrices, while
`RMSS(11), RMSS(12)` and `RMSS(14)` correspond to the right-right
entries. These entries need not be ordered in mass.