I wonder if there are any books or resources to start learning Materials modelling using methods
- density functional theory
- quantum monte carlo
- molecular dynamics
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This question is a bit old now, but hopefully my answer can complement Thomas's for anyone who comes across it.
While "materials" is not in the name of the book, I think great (though more advanced) introductions to these topics can be found in Thijssen's Computational Physics. What's nice about it is that it covers the theory, provides coding (as well as theoretical) exercises, and has sample programs for each chapter on the author's website (albeit in Fortran77, which is a language I abhor). You should definitely know how to program and at least the basics of numerical methods to start this book. 
For DFT, as mentioned in another post, the book starts you off with the Hartree problem, then you do the Hartree-Fock problem, and eventually planewave DFT.
For Quantum Monte Carlo, you start off with classical Monte Carlo integration and the Metropolis algorithm, before discussing a variety of modern QMC methods (VMC, DMC, PIMC).
For Molecular Dynamics, you start with a relatively simple symplectic integrator for a classical monatomic simulation, then move on to molecular systems, quantum systems, and eventually the Car-Parinello method (disclaimer: I didn't finish this section as it's not related to my own work).
It also covers a range of other useful (or at least interesting) topics, though mostly focused on matter modelling, from the Duffing oscillator to lattice field theory. Thijssen covers a broad range of topics and hence doesn't go into such gruesome detail, however, so this should really be treated as an introduction, after which you can read more specialised books and review articles in the areas that interest you. In addition to getting the satisfaction of writing some of these programs from scratch, I have found it to be helpful in understanding what the software suites (e.g. Molpro, CASINO) I use for these calculations actually do and how to use them more effectively.
: For an introduction to numerics, I personally used Ascher and Greif's Introduction to Numerical Methods, but this is not a matter modelling book. I have heard good things about Newman's and Koonin's books which are both more introductory as well and probably more interesting to people interested in matter modelling.