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##	sample MD pseudocode for shock compression simulation
##	written by Afnan Mostafa (let me know if you need a fully-fledged working script)
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# initialize simulation parameters
set units (metal), 3D periodic boundary conditions
set timestep (dt = 0.001 ps or finer dt for more precise simulation)

# load atomic structure
read atomic data
replicate system if needed (e.g., 2 x 1 x 30)

# define potential
set potential using pot_file.data

# compute per-atom energy and stress
calculate potential energy, atomic stress, von Mises stress, etc.

# energy minimization 
perform conjugate gradient minimization
perform box relaxation, couple xyz dimensions
save minimized structure

# initialize velocities (e.g., 300 K)
assign Gaussian velocity distribution

# equilibration phases
run NPT ensemble (50,000 steps)
run NVT ensemble (50,000 steps)
run NVE ensemble (50,000 steps)
save equilibrated system

# shock simulation setup
change z-boundary (shock propagation dir) to shrink-wrapped

# define piston and bulk regions
region piston block INF INF INF INF INF ${piston_zhi} units box
region bulk block INF INF INF INF ${piston_zhi} INF units box
set piston velocity (e.g., 4.0 km/s)
fix piston atoms (zero forces)

# perform shock simulation (NVE)
run NVE ensemble, apply piston velocity
record chunk-based profiles (density, temperature, pressure, velocity, etc.)

# output and thermodynamics
periodically print thermodynamics
save snapshots and output log files

# run shock simulation (N steps)
run N