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CFDEMcoupling-PFM/tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/DEM/in.liggghts_init
danielque 1f5c8f6492 add a tutorial for cfdemSolverIBContinuousForcing
simulating the deformation of a red blood cell (bonded particles) in
shear flow
2022-03-24 15:39:10 +01:00

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# Insert a RBC into a box, then induce shear flow
log ../DEM/log.liggghts
thermo_log ../DEM/post/thermo.txt
# bond parameter setup
variable rp equal 1.955 # sphere radius
variable ro equal 1 # bond outer radius multiplier
variable ri equal 0 # bond inner radius multiplier
variable rb equal 2*${ro}*${rp} # bond radius
variable lb equal 0.3090 # bond length multiplier
variable damp equal 300 # damping coefficient
# material properties
variable G equal 0.005333 # in-plane shear modulus of the membrane
variable Y equal 0.020426 # in-plane Young's modulus of the membrane
variable Sn equal $Y/3.91 # analogous Youngs modulus of the parallel bond
variable St equal $G/3.91 # analogous shear modulus of the parallel bond
variable Sben equal ${Sn}*10 # analogous bending modulus of the parallel bond
variable Stor equal ${Sn}*10 # analogous torsional modulus of the parallel bond
# atom type and style
atom_style hybrid granular bond/gran n_bondtypes 1 bonds_per_atom 6
atom_modify map array
# boundary
boundary p f p
# communication
newton off
communicate single vel yes
# units
units micro
#region and box creation
region domain block 0 45 0 22.5 0 22.5 units box
create_box 2 domain
# neighbors
neighbor 1 bin
neigh_modify exclude molecule all
neigh_modify delay 0
# material properties
fix m1 all property/global youngsModulus peratomtype 7.5e02 7.5e03
fix m2 all property/global poissonsRatio peratomtype 0.5 0.5
fix m3 all property/global coefficientRestitution peratomtypepair 2 1e-06 1e-03 1e-03 1e-06
fix m4 all property/global coefficientFriction peratomtypepair 2 0.3 0.1 0.1 0.3
# pair style
pair_style gran model hertz tangential history
pair_coeff * *
# bond parameters
bond_style gran
# N ro ri lb Sn_bond St_bond s_bend s_tor damp bn bt TYPE_OF_BOND sigma_break tau_break
bond_coeff 1 ${ro} ${ri} ${lb} ${Sn} ${St} ${Sben} ${Stor} ${damp} 2.65 0.0 1 1e50 1e50
# particle template, insertion region and bond formation
fix pts1 all particletemplate/multiplespheres 15485863 atom_type 1 &
density constant 1098 nspheres 10 ntry 1000000 spheres file ../DEM/data/spheres.txt scale 1 &
bonded yes/explicit &
nbond_pairs 10 &
1 2 &
2 3 &
3 4 &
4 5 &
5 6 &
6 7 &
7 8 &
8 9 &
9 10 &
10 1 &
bond_type 1
fix pdd1 all particledistribution/discrete 32452843 1 pts1 1.0
region bc1 block 0 45 0 22.5 0 22.5 units box
fix ins1 all insert/pack seed 32452867 distributiontemplate pdd1 &
maxattempt 10000 insert_every once overlapcheck yes vel constant 0.0 0.0 0.0 &
region bc1 particles_in_region 1 pos 22.5 11.25 11.25 ntry_mc 100000
run 1000
# set timestep
timestep 0.001
# check timestep
fix ts_check all check/timestep/gran 1000 0.1 0.1
# screen output
thermo_style custom step atoms numbond
thermo 10000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
dump dmp all custom 1000 ../DEM/post/dump*.liggghts &
id mol type x y z vx vy vz fx fy fz omegax omegay omegaz radius
compute b1 all property/local &
batom1x batom1y batom1z batom2x batom2y batom2z &
batom1 batom2 btype bforceX bforceY bforceZ
# x1 y1 z1 x2 y2 z2 id1 id2 bondtype f_bond[1] f_bond[2] f_bond[3]
dump bnd all local 1000 ../DEM/post/bonds*.bond1 &
c_b1[1] c_b1[2] c_b1[3] c_b1[4] c_b1[5] c_b1[6] &
c_b1[7] c_b1[8] c_b1[9] c_b1[10] c_b1[11] c_b1[12]
run 100000
write_restart ../DEM/post/restart/liggghts.restart