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The CTLSS code is an integrated three-dimensional cold-test and large-signal simulation suite. This paper treats the 3D cold-test portion of CTLSS, which is a general-geometry, frequency-domain, electromagnetic code that handles lossy materials with very high loss tangent. CTLSS handles both resonant eigenvalue problems and non-resonant driven frequency problems. Both resonant and non-resonant problems require the inversion of a linear matrix equation of the form, Ax=b, where the inclusion of lossy materials and Floquet boundary conditions causes the matrix operator A to become non-Hermitian and non-symmetric. CTLSS uses the Quasi-Minimal Residual (QMR) technique to handle these matrix inversions. For eigenvalue problems, the QMR algorithm is employed within a modified version of the Jacobi-Davidson method. The model supports the standard electric wall, magnetic wall, and periodic (Floquet) boundary conditions, as well as a perfectly-matched layer (PML) model for handling ports and outgoing-wave boundaries. Techniques to incorporate field drivers in ports with PML have been implemented, as well as the machinery needed to decompose fields in the port into waveguide modes, so that N-port systems may be analyzed with S parameters linking both ports and modes. This paper will describe code results obtained in simulations of numerous vacuum electron device types. CTLSS has been successful in predicting dispersion curves and coupling impedance of resonant modes, and more recently, in the computation of S parameters.