What tense to use in thesis when describing complex simulation models? I've researched the "rules" regarding use of tenses in scientific writing. However, I'm still not sure how to describe the simulations I've done during my thesis. 

Just a simple example: 


  1: An example model was developed to simulate the behavior during
  compression.


Here I'm describing something I did in the past, similar to an experiment, hence I'm using the past tense. 

Then I'll describe what happens during the simulation, or how specific properties of the simulation model were set. 


  2: The piston geometry is imported as a .stl-mesh. By moving the mesh in direction of the negative z-axis, the particles in the
  cylinder are compressed until...


I'm not sure about the tenses used in example 2. I could have also written: 


  3: The piston geometry was imported as a .stl-mesh. By moving the mesh in direction of the negative z-axis, the particles in the
  cylinder were compressed until...


I can't decide whether example 2 or 3 is the better choice.
I would say the present tense is appropriate if you are giving a description of how the model works in general.  The model itself is timeless; it will keep working the same way now and forever.

The past tense puts the emphasis on what you did in your specific project; it reads like a report.  You did it this way; someone else in the future might do something else.