# Removing Binned Velocities of Center of Mass (VCM) from Stress 

# This example shows how to remove rigid body motion from 
# binned stress calculations. This uses a combination of commands
# from compute chunk/atom, compute temp/chunk, compute 
# stress/atom and fix ave/time. We'll show how these commands 
# work in the context of a shockwave experiment on a cube of 
# atoms. To shock the cube, a rectangular region of atoms is 
# frozen, moved into the cube with a constant velocity along the
# x direction, and then unfrozen. As the shockwave begins 
# propagating, the body of the cube also moves along the x 
# direction. To better understand the stress dynamics of the 
# cube we remove the velocity component belonging to the overall 
# motion of each bin.

units		    metal
boundary        p p p
atom_style	    atomic
lattice		    fcc 5.3589
processors 		1 * *

# Defining regions for box and atoms.
# In this experiment an elongated simulation cell is 
# defined in the x direction to allow for non-periodic 
# motion of the atoms.

region		    box1 block -3 24 0 12 0 12 units lattice
region		    box2 block 0 12 0 12 0 12 units lattice

# Creating box and atoms

create_box	    1 box1
create_atoms    1 region box2

mass		    1 40.00

# Adding energy to the system

velocity        all create 600.0 9999

pair_style	    lj/cut 10 
pair_coeff	    1 1 0.04 3.405

# Begin time integration

timestep        2e-3

fix	            fix_nve all nve

thermo		    100

run             500

#--------------------------------------#
# Chunk, Stress, and VCM removal steps #
#--------------------------------------#

# 1. Create 20 equispaced bins sliced along the x direction.
# -"units reduced" normalizes the distance from 0.0 to 1.0
variable        nbins index 20
variable        fraction equal 1.0/v_nbins
variable        volfrac equal 1/(vol*${fraction}) 
compute         ch_id all chunk/atom bin/1d x lower ${fraction} units reduced 

# 2. Calculate temperature bins with VCM aka COM velocities removed.
compute         ch_temp_vcm all temp/chunk ch_id com yes

# 3. Compute per atom stress with VCM removed via temp-ID.
# -The velocities from specified temp-ID are used to compute stress.
# -Stress/atom units are pressure*volume! Optionally handled next step.
compute         atom_stress_vcm all stress/atom ch_temp_vcm

# 4. Divide out bin volume from xx stress component.
variable        stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})

# 5. Sum the per atom stresses in each bin.
compute         ch_stress_vcm all reduce/chunk ch_id sum v_stress

# 6. Average and output to file.
# -The average output is every 100 steps with samples collected 20 times with 5 step intervals.
fix             ave_stress_vcm all ave/time 5 20 100 c_ch_stress_vcm mode vector file stress_xx.out

#--------------------------------------#

# Piston compressing along x direction

region 			piston block -1 1 INF INF INF INF units lattice
group          	piston region piston
fix 			fix_piston piston move linear 5 0 0 units box # strain rate ~ 8e10 1/s 

thermo_style    custom step temp ke pe lx ly lz pxx pyy pzz econserve 

# Atom dump

# dump		    atom_dump all atom 50 dump.vcm

# # Image dumps

# dump		    2 all image 250 image.*.jpg type type &
# 		        axes yes 0.8 0.02 view 60 -30
# dump_modify	    2 pad 1

# # Movie dump

# dump		    3 all movie 125 movie.avi type type &
# 		        axes yes 0.8 0.02 view 60 -30
# dump_modify	    3 pad 1

run	            500

unfix           fix_piston

run             1500