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We give a comprehensive account of our proposed experimental method of using atoms or molecules in order to measure parameters of neutrinos still undetermined; the absolute mass scale, the mass hierarchy pattern (normal or inverted), the neutrino mass type (Majorana or Dirac), and the CP violating phases including Majorana phases. There are advantages of atomic targets, due to the closeness of available atomic energies to anticipated neutrino masses, over nuclear target experiments. Disadvantage of using atomic targets, the smallness of rates, is overcome by the macro-coherent amplification mechanism. The atomic or molecular process we use is a cooperative deexcitation of a collective body of atoms in a metastable level |e> emitting a neutrino pair and a photon; |e> -> |g> + gamma + nu_i nu_j where nu_i's are neutrino mass eigenstates. The macro-coherence is developed by trigger laser irradiation. We discuss aspects of the macro-coherence development by setting up the master equation for the target quantum state and propagating electric field. With a choice of heavy target atom or molecule such as Xe or I_2 that has a large M1 x E1 matrix element between |e> and |g>, we show that one can determine three neutrino masses along with the mass hierarchy pattern by measuring the photon spectral shape. If one uses a target of available energy of a fraction of 1 eV, Majorana CP phases may be determined. Our master equation, when applied to E1 x E1 transition such as pH_2 vibrational transition Xv=1 -> 0, can describe explosive PSR events in which most of the energy stored in |e> is released within a few nanoseconds. The present paper is intended to be self-contained explaining some details related theoretical works in the past, and further reports new simulations and our ongoing experimental efforts of the project to realize the neutrino mass spectroscopy using atoms/molecules., Comment: 85 pages. Accepted for publication in Progress of Theoretical and Experimental Physics