SPECTRUM code
I used the model by Richard O. Gray, called SPECTRUM (version 2.76). This is available from his web-site. The model can handle different stellar atmosphere models currently from spectral classes B to M.
This easy-to-use code runs under Windows with pre compiled executables (compiled under XP, runs under Windows 7 also?). The source code is in C, and can be compiled on any(?) Unix/Linux/Windows system. All relevant atomic data (abundances and quantum-mechanical data for the line transitions), and a few hydrostatic atmosphere models are included. More can be downloaded from other sources. The documantation is excellent.
The LTE approximation is adopted (local thermodynamic equilibrium), and plane parallel atmospheres (good for thin atmospheres compared to the stellar radius). Despite the limitations, this approach speeds up the computations, and can represent most of the main sequence stars, and possibly also more evolved stars. One can identify the element abundances using observed spectra (your observations), determine rotation rates, surface gravity and other essential properties. The input data files contain all the naturally occuring elements, along with 310 isotopes, and 15 diatomic molecules. Hyperfine structure is also supported. Thousands of spectral lines can be calculated (!) The atmospheres are assumed to be in hydrostatic equilibrium (non-expanding, non-pulsating atmospheres), although velocity gradients can be included to explore Doppler-shift effects and how these affect the spectral lines.
The code provides a very important smoothing option, so to that the model results can be compared to your observed spectra, with the given the instrument response/smearing.