LIGGGHTS WITH BONDS - beam example does not work

Hello,

I am new to liggghts, and for my project I need a DEM with implementation of a parallel bond similar to Potyondy and Cundall 2004.
I've found a third-party implementation of parallel bonds in LIGGGHTS - https://github.com/richti83/LIGGGHTS-WITH-BONDS
I've installed and run a simple beam example from that repo, but it seems that bonds do not exert proper forces and moments - 10 out of 11
remain in place, and 11-th moves with an acceleration. However, according to script output everything should work fine.

Did anyone face that issue with this particular implementation? Any insight is deeply appreciated.
Below I attach a console output and a dump file - they might be of some clue of what's happening.

Liggghts console output ( lmp < beam.bonds )

LIGGGHTS (Version LIGGGHTS-PUBLIC 3.3.0, compiled 2017-04-14-13:43:02 by ostanin, git commit 679ce24504b1922e24d3adc8c8713c98e59a1aaa based on LAMMPS 23 Nov 2013)
Created orthogonal box = (-5.334 -1 -5.334) to (5.334 1 1)
1 by 1 by 1 MPI processor grid
WARNING: Bond granular: This is a beta version - be careful! (../bond_gran.cpp:83)
68947572900
25920150556.026
0.00133901269899076
0.129717114648959
271447137401.575
65147312976.3781
Lattice spacing in x,y,z = 0.508 0.508 0.508
Created 11 atoms
Setting up run ...
Memory usage per processor = 8.23669 Mbytes
Step Atoms KinEng CPU
0 11 0 0
1 11 0 1.5974045e-05
Loop time of 3.8147e-05 on 1 procs for 1 steps with 11 atoms

Pair time (%) = 5.96046e-06 (15.625)
Bond time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 9.53674e-07 (2.5)
Outpt time (%) = 2.71797e-05 (71.25)
Other time (%) = 4.05312e-06 (10.625)

Nlocal: 11 ave 11 max 11 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 27
Ave neighs/atom = 2.45455
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
11 atoms in group bonded
Setting atom values ...
11 settings made for density
11 settings made for diameter
Setting up run ...
Memory usage per processor = 8.23798 Mbytes
Step Atoms KinEng CPU
1 11 0 0
2 11 0 1.3113022e-05
Loop time of 3.19481e-05 on 1 procs for 1 steps with 11 atoms

Pair time (%) = 5.00679e-06 (15.6716)
Bond time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 2.28882e-05 (71.6418)
Other time (%) = 4.05312e-06 (12.6866)

Nlocal: 11 ave 11 max 11 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19 ave 19 max 19 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 19
Ave neighs/atom = 1.72727
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
1 atoms in group freezed
1 atoms in group tipball
Setting up run ...
Memory usage per processor = 8.23798 Mbytes
Step Atoms KinEng CPU
2 11 0 0
3 11 0 1.1920929e-05
Loop time of 3.00407e-05 on 1 procs for 1 steps with 11 atoms

Pair time (%) = 5.00679e-06 (16.6667)
Bond time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 9.53674e-07 (3.1746)
Outpt time (%) = 2.19345e-05 (73.0159)
Other time (%) = 2.14577e-06 (7.14286)

Nlocal: 11 ave 11 max 11 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19 ave 19 max 19 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 19
Ave neighs/atom = 1.72727
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
11 atoms in group nve_group
Setting up run ...
Memory usage per processor = 9.15403 Mbytes
Step Atoms numbond
3 11 0
creating bond btw atoms 0 and 1 (i has now 1 bonds) at step 4
creating bond btw atoms 1 and 0 (i has now 1 bonds) at step 4
creating bond btw atoms 1 and 2 (i has now 2 bonds) at step 4
creating bond btw atoms 2 and 1 (i has now 1 bonds) at step 4
creating bond btw atoms 2 and 3 (i has now 2 bonds) at step 4
creating bond btw atoms 3 and 2 (i has now 1 bonds) at step 4
creating bond btw atoms 3 and 4 (i has now 2 bonds) at step 4
creating bond btw atoms 4 and 3 (i has now 1 bonds) at step 4
creating bond btw atoms 4 and 5 (i has now 2 bonds) at step 4
creating bond btw atoms 5 and 4 (i has now 1 bonds) at step 4
creating bond btw atoms 5 and 6 (i has now 2 bonds) at step 4
creating bond btw atoms 6 and 5 (i has now 1 bonds) at step 4
creating bond btw atoms 6 and 7 (i has now 2 bonds) at step 4
creating bond btw atoms 7 and 6 (i has now 1 bonds) at step 4
creating bond btw atoms 7 and 8 (i has now 2 bonds) at step 4
creating bond btw atoms 8 and 7 (i has now 1 bonds) at step 4
creating bond btw atoms 8 and 9 (i has now 2 bonds) at step 4
creating bond btw atoms 9 and 8 (i has now 1 bonds) at step 4
creating bond btw atoms 9 and 10 (i has now 2 bonds) at step 4
creating bond btw atoms 10 and 9 (i has now 1 bonds) at step 4
Created 10 bonds at timestep 4
4 11 10
Loop time of 0.00067997 on 1 procs for 1 steps with 11 atoms

Pair time (%) = 6.91414e-06 (1.01683)
Bond time (%) = 5.96046e-06 (0.876578)
Neigh time (%) = 0.000154018 (22.6508)
Comm time (%) = 1.90735e-06 (0.280505)
Outpt time (%) = 2.19345e-05 (3.22581)
Other time (%) = 0.000489235 (71.9495)

Nlocal: 11 ave 11 max 11 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19 ave 19 max 19 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 19
Ave neighs/atom = 1.72727
Ave special neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 0

--------------------------------------------------------------

Sample output - liggghts10000.dump:

ITEM: TIMESTEP
10000
ITEM: NUMBER OF ATOMS
11
ITEM: BOX BOUNDS ff ff ff
-5.334 5.334
-1 1
-5.334 1
ITEM: ATOMS id type x y z vx vy vz fx fy fz omegax omegay omegaz radius
1 1 0 0 0 0 0 0 0 0 0 0 0 0 0.254
2 1 0.508 0 1.48129e-14 6.30804e-09 0 3.39765e-13 3.85896e-05 0 -1.47972e-10 0 -1.35825e-12 0 0.254
3 1 1.016 0 6.83012e-14 1.39516e-08 0 9.36076e-13 7.30956e-05 0 -9.91147e-11 0 -8.37722e-13 0 0.254
4 1 1.524 0 -2.12559e-13 2.23462e-08 0 -2.38512e-12 8.90979e-05 0 5.76973e-10 0 1.34245e-11 0 0.254
5 1 2.032 0 9.26154e-13 3.11058e-08 0 9.89466e-12 8.35655e-05 0 -1.34985e-09 0 -6.04882e-11 0 0.254
6 1 2.54 0 -4.11605e-12 3.92351e-08 0 -4.30539e-11 6.37116e-05 0 1.85856e-09 0 2.65882e-10 0 0.254
7 1 3.048 0 1.83001e-11 4.57086e-08 0 1.89332e-10 3.94711e-05 0 3.97163e-10 0 -1.17386e-09 0 0.254
8 1 3.556 0 -8.13352e-11 5.00132e-08 0 -8.36927e-10 1.90586e-05 0 -1.12861e-08 0 5.20011e-09 0 0.254
9 1 4.064 0 3.61391e-10 5.22827e-08 0 3.7104e-09 6.66768e-06 0 3.1982e-08 0 -2.30821e-08 0 0.254
10 1 4.572 0 -1.60554e-09 5.31237e-08 0 -1.64759e-08 1.86969e-06 0 -2.20502e-08 0 1.02552e-07 0 0.254
11 1 5.08 0 -0.011991 -2.00447e-08 0 -0.239916 0 0 -444.822 0 1.32353e-07 0 0.254