ERROR: Atom types must start from 1 for granular simulations (../properties.cpp:120)

Submitted by ___duffy__ on Sun, 02/04/2018 - 16:06

Hi,
I'm trying to modify the bin flow tutorial example so that a fixed number of particles will be loaded from a data file like the "in.hydrogel_default" example in folder hydrogel_multicontact.
So, I deleted

region domain block -0.138 0.138 -0.138 0.138 -0.0045 0.43 units box
create_box 2 domain

and inserted
read_data data/input_06.data

Input_06.data is a modification of input.data given in the hydrogel_multicontact.
The modification is change of lo's and hi's to accommodate the hopper.stl container geometry.
-0.1400 0.1701 xlo xhi
-0.1400 0.1701 ylo yhi
-0.0101 0.4101 zlo zhi

Here's the error I obtained.
I studied the data again but I could not find any problem with regard to atom type number.
Atom type number 1 appears in input_06.data.
I have attached the in.* data file and particle data file used.
Any suggestions are greatly appreciated to avoid this error.
Thank you in advance.
Regards,
Akio Miyoshi

LIGGGHTS (Version LIGGGHTS-PUBLIC 3.7.0, compiled 2017-11-15-09:57:03 by miyoshi, git commit c449f30b63c5eec5c8053a67dccd892fe2c5cef2)
units si
atom_style sphere
atom_modify map array

boundary f f f

newton off
communicate single vel yes

#processors 2 2 3

# fixed number of particles
read_data data/input_06.data
orthogonal box = (-0.14 -0.14 -0.0101) to (0.1701 0.1701 0.4101)
1 by 1 by 1 MPI processor grid
514 atoms
514 velocities

neighbor 0.003 bin

neigh_modify every 1 check no

fix m1 all property/global youngsModulus peratomtype 2.5e7 2.5e7
fix m2 all property/global poissonsRatio peratomtype 0.25 0.25

fix m3 all property/global coefficientRestitution peratomtypepair 2 0.5 0.5 0.5 0.5
fix m4 all property/global coefficientFriction peratomtypepair 2 0.2 0.175 0.175 0.5

#read_data

fix cad1 all mesh/surface file hopper.stl type 2 scale 0.0005

#fix geometry all wall/gran/hertz/history mesh n_meshes 1 meshes cad1 old data format 2018/01/25
fix geometry all wall/gran model hertz tangential history mesh n_meshes 1 meshes cad1

#fix stopper all wall/gran/hertz/history primitive type 2 zplane 0.0 old data format 2018/01/25
fix stopper all wall/gran model hertz tangential history primitive type 2 zplane 0.0

#pair_style gran/hertz/history Old data format 2018/01/25 old data format 2018/01/25
pair_style gran model hertz tangential history

pair_coeff * *

fix integrate all nve/sphere

fix grav all gravity 9.81 vector 0.0 0.0 -1.0

timestep 0.00001

thermo_style custom step atoms ke cpu

thermo 10000

thermo_modify norm no lost ignore

fix ctg all check/timestep/gran 1 0.01 0.01
run 1
WARNING: It is heavily recommended to use 'neigh_modify delay 0' with granular pair styles (../pair_gran.cpp:237)
Setting up run at Sun Feb 4 19:34:09 2018

WARNING: Fix mesh: Mesh contains highly skewed element, moving mesh (if used) will not parallelize well (../surface_mesh_I.h:656)
Memory usage per processor = 9.60556 Mbytes
Step Atoms KinEng CPU
0 514 4.5519325e-10 0
WARNING: time-step is 29.977398 % of rayleigh time (../fix_check_timestep_gran.cpp:200)
WARNING: time-step is 20.070102 % of hertz time (../fix_check_timestep_gran.cpp:208)
WARNING: time step too large or skin too small - particles may relatively travel a distance of 0.010237 per time-step, but skin is 0.003000 (../fix_check_timestep_gran.cpp:217)
WARNING: time step way too large - particles relativley move further than the minimum radius in one step (../fix_check_timestep_gran.cpp:226)
1 514 49.434455 0.0008687973
Loop time of 0.000928879 on 1 procs for 1 steps with 514 atoms, finish time Sun Feb 4 19:34:09 2018

Pair time (%) = 0.000226021 (24.3326)
Neigh time (%) = 0 (0)
Comm time (%) = 9.53674e-07 (0.102669)
Outpt time (%) = 6.69956e-05 (7.21253)
Other time (%) = 0.000634909 (68.3522)

Nlocal: 514 ave 514 max 514 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: 2015 ave 2015 max 2015 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2015
Ave neighs/atom = 3.92023
Neighbor list builds = 0
Dangerous builds = 0
unfix ctg

#dump dumpstl all stl 10000 dump*.stl
#dump dmp all custom 10000 dump.1 id type type x y z ix iy iz vx vy vz # fx fy fz omegax omegay omegaz radius
dump dmp all custom/vtk 100 post/binFlow*.vtk id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius
dump dmp2 all mesh/vtk 100 post/binFlow_mesh*.vtk id vel

run 150000 upto
WARNING: It is heavily recommended to use 'neigh_modify delay 0' with granular pair styles (../pair_gran.cpp:237)
Setting up run at Sun Feb 4 19:34:09 2018

Memory usage per processor = 9.60589 Mbytes
Step Atoms KinEng CPU
1 514 49.434455 0
10000 4 0.0012194804 0.65759492
20000 1 5.7786497e-05 1.2478249
30000 1 2.6980872e-05 1.777688
40000 0 0 2.094157
50000 0 0 2.376797
60000 0 0 2.633101
70000 0 0 2.8930559
80000 0 0 3.1327219
90000 0 0 3.392621
100000 0 0 3.663228
110000 0 0 3.9082811
120000 0 0 4.22001
130000 0 0 4.468231
140000 0 0 4.7321601
150000 0 0 4.983022
Loop time of 4.98312 on 1 procs for 149999 steps with 0 atoms, finish time Sun Feb 4 19:34:14 2018

Pair time (%) = 0.0589457 (1.18291)
Neigh time (%) = 0.251701 (5.05108)
Comm time (%) = 0.0237813 (0.477237)
Outpt time (%) = 2.68772 (53.9364)
Other time (%) = 1.96098 (39.3524)

Nlocal: 0 ave 0 max 0 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: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Neighbor list builds = 14999
Dangerous builds = 0

unfix stopper
run 300000
WARNING: It is heavily recommended to use 'neigh_modify delay 0' with granular pair styles (../pair_gran.cpp:237)
ERROR: Atom types must start from 1 for granular simulations (../properties.cpp:120)

AttachmentSize
Binary Data in.* file and read_data file.19.12 KB

___duffy__ | Sun, 02/04/2018 - 23:59

Hi,
The particles of type 1 just scattered and were gone.
And the type 1 particles are missing.
This is a natural physical phenomenon and not a problem.
Thank you.