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These are warning messages that can be safely ignored unless the
negative or imaginary charge is sizable, let us say of the order of
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.
Paolo Giannozzi
2009-10-01