``warning : negative or imaginary charge...'', or ``...core charge ...'', or ``npt with rhoup< 0...'' or ''rhodw< 0...''

These are warning messages that can be safely ignored unless the negative or imaginary charge is sizable, let us say O(0.1). If it is, something seriously wrong is going on. Otherwise, the origin of the negative charge is the following. When one transforms a positive function in real space to Fourier space and truncates at some finite cutoff, the positive function is no longer guaranteed to be positive when transformed back to real space. This happens only with core corrections and with ultrasoft pseudopotentials. In some cases it may be a source of trouble (see next point) but it is usually solved by increasing the cutoff for the charge density.