Fix gradient evaluation when one of coordinates is close to another #1208
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Fix #986
If one of coordinates close to another in another atom, S(ii,jj) tends to zero, at the same time corresponding H0 is also tends to zero and therefore H0(k)/S(ii,jj) is constant. But since S(ii,jj) was skipped, the H(ii,jj) becomes zero that is incorrect.