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If I get a born effective charge：

BORN EFFECTIVE CHARGES (including local field effects)
------------------------------------------------------
ion 1
1 2.98061 0.03000 0.00000
2 -0.04000 2.98061 0.00000
3 0.00000 -0.00000 2.95148

when the displacement of the first ion is (0.01, 0.0, 0.0)，is the dipole moment 0.0003 or -0.0004?

You can find this information in the code: pead.F
Here is the point at which the Born effective charges are computed (when using PEAD): F_INIT(3,NIONS) and TIFOR(3,NIONS) contain the initial and final forces (after an electric field is applied).

Here is the line where they are printed: so the first number on each line (1,2,3) corresponds to the (x,y,z) direction of the electric field.
To answer your question:
If you displace ion 1 along (1.0, 0.0, 0.0) you should get a dipole moment of (2.98061,-0.04000,0.0).

Dear Henrique,
Thank you!