Add miniMD setup reading data from file

ast/arrays.py

ast/block.py

ast/cast.py

ast/expr.py

ast/lit.py

ast/loops.py

ast/math.py

ast/properties.py

ast/sizeof.py

ast/transform.py

ast/variables.py

data/minimd_setup_4x4x4.input

output/.gitignore

particle.py

sim/particle_simulation.py

sim/read_from_file.py

sim/timestep.py