Hybrid Monte Carlo, Simon Duane, A. D. Kennedy, Brian J. Pendleton, and Duncan Roweth, 1987Physics Letters B, Vol. 195 (Elsevier)DOI: 10.1016/0370-2693(87)91197-X - The original paper introducing Hybrid Monte Carlo, the foundation of HMC.
MCMC Using Hamiltonian Dynamics, Radford M. Neal, 2011Handbook of Markov Chain Monte Carlo (Chapman & Hall/CRC)DOI: 10.1201/b10905-6 - A widely referenced chapter providing a detailed discussion of HMC theory and practice.
Bayesian Data Analysis, Andrew Gelman, John B. Carlin, Hal S. Stern, David B. Dunson, Aki Vehtari, and Donald B. Rubin, 2013 (Chapman and Hall/CRC)DOI: 10.1201/b16018 - A standard textbook in Bayesian statistics with comprehensive coverage of MCMC methods, including HMC.