Dear lammps experts,
I have applied compute chunk/atom, temp/chunk and chunk/spread/atom respectively as follow in a 2 dimensional simple MD simulation:
1-compute mychunk all chunk/atom bin/2d x lower 2 y lower 2 nchunk every limit 0 ids every compress yes discard yes units box
2-compute temp_chunk particle temp/chunk mychunk temp com yes
3-compute 1 particle chunk/spread/atom mychunk c_temp_chunk (I think something has been missed here!)
4-dump 2 all custom 100 dump id x y z c_1
but unfortunately c_1 does not show temperature of each chunk.so please let e know whether there is any wrong in my commands?!
below you can find above commands in a context of my file
#Phase 1 ------------------------------------------Simulation main setup----------------------------------
dimension 2
units metal
atom_style atomic
boundary p f p
lattice sq2 3.597
variable vy equal -10
variable radius equal 175
variable diameter equal “2*v_radius”
variable n equal 175 # BoxxX and BoxY becomes 189.3
variable a1 equal 3.597
variable a2 equal 3.597
variable a3 equal 3.597
variable boxx equal “v_nv_a1"
variable x0 equal "0.5v_boxx”
variable y0 equal “0.5v_boxy"
variable subs_thick equal "36v_a2”
variable subslow_thick equal “0.1v_a2"
variable y_gap equal "0.2v_radius”
variable distance equal “v_subs_thick+v_subslow_thick+v_y_gap+v_radius”
variable boxy equal “v_distance+v_diameter+3*v_diameter”
#simulation box
region box block 0 {boxx} 0 {boxy} -0.5 0.5 units box
create_box 1 box
#particle
region particle cylinder z {x0} {distance} ${radius} -0.5 0.5 units box #r=172.5 Ang =17.25 nm===>d=34.5 nm
create_atoms 1 region particle
group particle region particle
mass 1 58.69
#substrate
region substrate block 0 {boxx} {subslow_thick} ${subs_thick} -0.5 0.5 units box
create_atoms 1 region substrate
group substrate region substrate
mass 1 58.69
#lower_substrate
region lower_substrate block 0 {boxx} 0 {subslow_thick} -0.5 0.5 units box
create_atoms 1 region lower_substrate
group lower_substrate region lower_substrate
mass 1 58.69
group model union particle substrate
#–Phase 2-------------------------------------- Potential-----------------------------------------------
pair_style eam
pair_coeff 1 1 Cu_u3.eam # EAM parameters for Cu-Cu
#—Phase 3----------------------------------------Compute--------------------------
compute mychunk model chunk/atom bin/2d x 0 30 y 0 30 nchunk every limit 0 ids every compress yes discard no units box
compute temp_chunk model temp/chunk mychunk temp
compute 1 model chunk/spread/atom mychunk c_temp_chunk
compute kecom_chunk model temp/chunk mychunk kecom
#----Phase 4-------------------------------------Initial Equilibration at 300K ----------------------------------------
reset_timestep 0
timestep 0.005 # Achtung! in metal unit time-step is by default 1 picoseconds scale
velocity all create 300 12345 mom yes rot no
fix 1 lower_substrate setforce 0.0 0.0 0.0
fix 2 model nve
fix 3 substrate temp/rescale 100 1000.0 300.0 10.0 1.0
fix 4 particle temp/rescale 100 1000.0 1000.0 10.0 1.0
thermo 100
thermo_modify lost ignore flush yes
neighbor 2.0 bin
neigh_modify delay 5
run 100
unfix 3
unfix 4
fix 5 particle temp/rescale 100 300.0 300.0 10.0 1.0
fix 6 substrate temp/rescale 100 300.0 300.0 10.0 1.0
thermo 100
thermo_modify lost ignore flush yes
neighbor 2.0 bin
neigh_modify delay 5
run 100
unfix 5
#----Phase 5---------------------------------------Particle Impact at the room temperature --------------------
velocity particle set 0 {vy} 0 units box# *100m/s
thermo 100
dump 1 all xyz 100 dump-{diameter}-{vy}.xyz
dump 2 all custom 100 dump_{vy} id x y z c_1
run 10000
with the best regards,
Bahman