# minimum Working Example for Simulation of clump using molecule

# 1. Setup simulation environments
units            si
dimension        3
atom_style       hybrid sphere molecular

boundary         f f f
newton           off
processors       * * 2 numa_nodes 4 #grid numa

# 2. Setup Communication and Neighboring list
#comm_modify      mode single vel yes #NG
#comm_modify      mode single vel yes cutoff 0.008 #NG
comm_modify      mode single vel yes cutoff 0.009 #OK
neigh_modify    delay 0 every 10 check yes once no cluster no exclude molecule/intra all page 10000000 one 20000 # binsize 0.0005

# 3. Setup Packages
package          omp 5
suffix           omp

# 4. Setup variables
variable         crit_dt      equal 1e-6

# 5. Setup Domain
region           domain3D block -0.025 0.025 -0.025 0.025 0.0 0.025
create_box       2 domain3D

# 5. Read atom and molecule data
molecule         clumps m1.data scale 1E-3 m2.data scale 1E-3           # Readout two template for molecule
region           insertionRegion block -0.024 0.024 -0.024 0.024 0.01 0.024     # Set pouring Space

# 8. Apply gravity
fix              grav_acc all gravity 9.81 vector 0.0 0.0 -1.0
fix              viscousDamping all viscous 0.0001

fix              makeClumps all rigid/small/omp molecule mol clumps gravity grav_acc
fix              pourClumps all pour 10 1 4767548 region insertionRegion dens 2700 2700 mol clumps molfrac 0.5 0.5 rigid makeClumps

# 6. Decalre mocules is composed of sphere : DOF adjust ment not to calculate DOF <=0
compute          adjustDOF all temp/sphere
thermo_modify    temp adjustDOF

# 7. Setup interactions btw atoms (molecule)
pair_style       gran/hertz/history/omp 1.75e9 NULL 50.0 NULL 0.5 1
pair_coeff       * *

fix              bottomPlate all wall/gran hertz/history 1.75e9 NULL 50.0 NULL 0.5 1 &
                 zplane 0.0 NULL

# 9. Preparation for run
timestep         ${crit_dt}
run              100000