Molecular clouds act as targets for cosmic rays (CR), revealing their presence through either gamma-ray emission due to proton-proton interactions, and/or through the ionization level in the cloud, produced by the CR flux. The ionization rate is a unique tool, to some extent complementary to the gamma-ray emission, in that it allows to constrain the CR spectrum especially for energies below the pion production rate ($approx 280$ MeV). Here we study the effect of ionization on $H_2$ clouds due to both CR protons and electrons, using the fully relativistic ionization cross sections, which is important to correctly account for the contribution due to relativistic CRs. The contribution to ionization due to secondary electrons is also included self-consistently. The whole calculation has been implemented into a numerical code which is publicly accessible through a web-interface. The code also include the calculation of gamma-ray emission once the CR spectrum
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