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I need to be able to set the properties of the materials (density, size etc) and see what happens according to laws in Physics when landmasses collide each others, with or without bodies of water, such as in the plate tectonics theory.

Can you recommend a software for this?

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There are a number of software packages out there that you can use -- most are curated by the Computational Infrastructure in Geodynamics initiative (see http://www.geodynamics.org). The fundamental question you will need to answer is what time scale and material description you want to investigate.

For example, if you care about short term (at the intraseismic time scale) deformation, then PyLith is probably the code you want to look at. On the other hand, if you care about much longer time scales, you could take a look at ASPECT, which has been used for these sorts of simulations. There are many other codes in this area, and they all have their reason and realm of applicability, depending on what exactly you want to do.

(Full disclosure: I'm one of the authors and maintainers of ASPECT.)

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