Cross-link bond formation

Submitted by SHUBHAM AGARWAL on Sat, 10/03/2020 - 22:52

Hello
I am trying to simulate a fiber fall. Once they hit the ground, i want to cross-link the fibers based on a critical distance. For cross link bond formation, i am using bond/create command. How wever I an getting the folloing error:
ERROR: Invalid fix style: "bond/create" (../modify.cpp:852)

Thanks
SHUBHAM

Following is my input script:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
atom_style sphere
atom_modify map array sort 0 0
boundary m m m
newton off

communicate single vel yes

#PUBLIC version only supports serial execution
#processors 1 1 1

units si

region reg block -0.3 0.3 -0.3 0.3 0. 0.5 units box
create_box 1 reg

neighbor 0.004 bin
neigh_modify delay 0

#Material properties required for new pair styles

fix m1 all property/global youngsModulus peratomtype 1.e7
fix m2 all property/global poissonsRatio peratomtype 0.45
fix m3 all property/global coefficientRestitution peratomtypepair 1 0.3
fix m4 all property/global coefficientFriction peratomtypepair 1 0.5
fix m5 all property/global characteristicVelocity scalar 2.

#New pair style
pair_style gran model hertz tangential history #Hertzian without cohesion
pair_coeff * *

timestep 0.00001

fix gravi all gravity 9.81 vector 0.0 0.0 -1.0

fix zwalls all wall/gran model hertz tangential history primitive type 1 zplane 0.0

#distributions for insertion
fix pts1 all particletemplate/multisphere 15485863 atom_type 1 density constant 2500 nspheres 10 ntry 1000000 spheres file mult.txt scale 0.01 type 1
fix pdd1 all particledistribution/discrete 15485867 1 pts1 1.0

#region and insertion
region bc cylinder z 0.0 0.0 0.25 0.1 0.4 units box

fix ins all insert/pack seed 32452843 distributiontemplate pdd1 vel constant 0. 0. -1. &
insert_every once orientation random overlapcheck yes region bc ntry_mc 10000 volumefraction_region 0.3

#integrator for multisphere rigid bodies
fix integr all multisphere

#output settings, include total thermal energy
compute 1 all erotate/sphere
fix ts all check/timestep/gran 1000 0.1 0.1
thermo_style custom step atoms ke c_1 f_ts[1] f_ts[2] vol
thermo 1000
thermo_modify lost ignore norm no

run 1

#insert the first particles so that dump is not empty
dump dmp all custom/vtk 800 post/fiber_*.vtk id type mol x y z vx vy vz fx fy fz omegax omegay omegaz radius

#insert particles
run 40000 upto

fix cross all bond/create 10 1 1 2.1 1
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

mschramm | Sun, 10/04/2020 - 03:59

Hello,
fix bond/create is not part of the public release.
You will need to use a third party release with the bonded model incorporated in it.
See
LIGGGHTS-WITH-BONDS
or
LIGGGHTS_Flexible_Fibers

If you want to use the bond model, you will not be able to use the multisphere atom type while using a bond/gran atom type.

SHUBHAM AGARWAL | Sun, 10/04/2020 - 16:58

Hi
I am using LIGGGHTS_Flexible_Fibers version.
I guess I need to switch off the multi-sphere

SHUBHAM AGARWAL | Mon, 10/05/2020 - 21:48

Hi
To run the simulation, I am using the following command in UBUNTU:
mpirun -np 4 lmp_1234 -in in.fiber
in.fiber is the input file, lmp_1234 is the name for compiled liggghts

Error I am getting is the following:
Invalid fix style: "bond/create" (../modify.cpp:852)

mschramm | Mon, 10/05/2020 - 23:20

Hello
For the bond formation, use the following fix
# every itype jtype cutoff btype newperts
fix bondcr all bond/create/gran 1 1 1 ${bond_skin} 1 6

bond_skin would be your critical distance. Note that this is an absolute distance and does not take into account the radius of a particle.
You can take into account the radius of the sphere by using
fix bondcr all bond/create/gran 1 1 1 ${bond_skin} 1 6 doNorm yes
Here, bond_skin is a multiplier for kissing spheres, set bond_skin to 1.1.