Run only once: after running RAYINVR, you can not change the v.in file in anyway if you intend to run DMPLSTSQR afterwards. And you must not run DMPLSTSQR more than once without first running RAYINVR again, otherwise twice the model perturbation will be added to the current model. Specifying model uncertainties: the main purpose of this is as a weighting to account for the difference in magnitude of velocity and depth of boundary values and thereby equalize their relative importance during the inversion. If different uncertainties are required for specific boundary or velocity nodes, the file i.out is edited to incorporate the appropriate uncertainties and the values of velunc and/or bndunc are set equal to zero. Fixed vertical velocity gradient: if the vertical velocity gradient is fixed in a layer which contains a pinchout , there may be problems in determining the updated lower layer velocities in a few special cases. A warning is given and these parameters should be checked after the inversion. Inversion of layer pinchouts: in a few special cases there are bugs in the inversion code when attempting to invert model parameters associated with a layer pinchout; check these parameters after the inversion.