  A method and code for calculations of diatomic molecules in the external
variable electromagnetic field have been developed. Code applied for
calculation of systematics in the electron's electric dipole moment search
experiment on ThO $H^3\Delta_1$ state related to geometric phases, including
dependence on $\Omega$-doublet, rotational level, and external static electric
field. It is found that systematics decrease cubically with respect to the
frequency of the rotating transverse component of the electric field.
Calculation confirms that experiment on ThO $H^3\Delta_1$ state is very robust
against systematic errors related to geometric phases.
