Superquadric for liggghts public

Submitted by Sherif on Fri, 05/14/2021 - 00:22

I read in restrictions for atom_style command document (https://www.cfdem.com/media/DEM/docu/atom_style.html?highlight=superquad...) that superquadric style is not available yet for public version?

Is that true or the document is not updated?

Sherif | Fri, 05/14/2021 - 00:41

I can run scripts with my public version having superquadric style in atom_style and contact model commands. I'm afraid that the results I get are for spheres not for superquadric particles?

Sherif | Sat, 05/15/2021 - 12:41

Thanks a lot Mathew for your reply.

Kashminder | Mon, 02/28/2022 - 21:32

I am running a simple superquadric code as follows:
units micro
atom_style superquadric
atom_modify map array
communicate single vel yes

boundary f f f
newton off

echo both

read_data velo

neighbor 0.001 bin
neigh_modify delay 0

# Material properties required for new pair styles

fix m1 all property/global youngsModulus peratomtype 1e8
fix m2 all property/global poissonsRatio peratomtype 0.24
fix m3 all property/global coefficientRestitution peratomtypepair 1 0.97
fix m4 all property/global coefficientFriction peratomtypepair 1 0.3
fix m5 all property/global characteristicVelocity scalar 1
#fix m6 all property/global cohesionEnergyDensity peratomtypepair 1 3e-5

# pair style

pair_style gran model hertz tangential history surface superquadric
pair_coeff * *

variable vx equal 0.0
variable vy equal 0.0
variable vz equal 0.0

# timestep, gravity
timestep 0.00001 # 1e-11 second time step

fix ali all addforce 0 0 0.1
#fix gravi all gravity 0.00000981 vector 0.0 0.0 -1.0

fix ts_check all check/timestep/gran 1000 0.1 0.1

#fix ot all wall/region reg lj126 0.000000005 0.000000005 0.00000000005

# apply nve integration to all particles that are inserted as single particles
fix 1 all nve/superquadric integration_scheme 1

# screen output
#compute rke all erotate/sphere update_on_run_end yes

#compute 3 all ke/atom update_on_run_end yes
thermo_style custom step time atoms ke #c_rke vol v_t v_theta1 v_teq v_vint v_rad_d #v_Khyd#v_deltaD#v_pic v_bic v_ux v_uy v_uz
thermo 10000
thermo_modify norm no lost ignore
compute_modify thermo_temp dynamic yes

# insert the first particles so that dump is not empty
#dump dmp all custom/vtk 10000 post/sph_*.vtk id type x y z vx vy vz #v_twitterx v_twittery v_twitterz v_ur v_ux v_uy v_uz vx vy vz fx fy fz v_int_for v_int_for11# v_forcevander1#v_addedFx v_addedFy v_addedFz v_orgFx v_orgFy v_orgFz # v_intx v_intx v_intx v_forcex v_forcey v_forcez v_deltaD v_comx v_comy v_comz v_vr v_forcezzz v_forcexx_x v_forcexz #v_int_for #v_intx# v_lmbda v_zeq v_pic v_pic1 v_bic1 v_nic1 v_J0 v_ueq_r v_ueq_z v_Jeq v_heq v_hdot v_req v_h v_zeq v_deltaD #v_theta v_heq v_hdot v_req v_h v_zeq
run 10000

run 212000000 # 1e-3 seconds run

and data file is

1 atoms
0 bonds
1 atom types
0 bond types

-300 300 xlo xhi
-300 300 ylo yhi
-300 300 zlo zhi

Atoms # full atom id atom type diameter density xyz(for sphere) #velocity(atom-ID vx vy vz wx wy wz)

1 1 1 1.5 2 -47.2 0 2.65

Velocities

1 0 0 0 0 0 0

BUT GETTING ERROR :
read_data velo
Reading data file ...
orthogonal box = (-300 -300 -300) to (300 300 300)
1 by 1 by 1 MPI processor grid
[egr-u-mn-hz-01:18484] *** Process received signal ***
[egr-u-mn-hz-01:18484] Signal: Segmentation fault (11)
[egr-u-mn-hz-01:18484] Signal code: Address not mapped (1)
[egr-u-mn-hz-01:18484] Failing at address: (nil)
[egr-u-mn-hz-01:18484] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7f1edf64f8a0]
[egr-u-mn-hz-01:18484] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x49b73)[0x7f1edf295b73]
[egr-u-mn-hz-01:18484] [ 2] lmp380(+0xd9036)[0x56004585b036]
[egr-u-mn-hz-01:18484] [ 3] lmp380(+0x295c69)[0x560045a17c69]
[egr-u-mn-hz-01:18484] [ 4] lmp380(+0x29c108)[0x560045a1e108]
[egr-u-mn-hz-01:18484] [ 5] lmp380(+0x2143ae)[0x5600459963ae]
[egr-u-mn-hz-01:18484] [ 6] lmp380(+0x211209)[0x560045993209]
[egr-u-mn-hz-01:18484] [ 7] lmp380(+0x211a66)[0x560045993a66]
[egr-u-mn-hz-01:18484] [ 8] lmp380(+0xabc1c)[0x56004582dc1c]
[egr-u-mn-hz-01:18484] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f1edf26db97]
[egr-u-mn-hz-01:18484] [10] lmp380(+0xaceda)[0x56004582eeda]
[egr-u-mn-hz-01:18484] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node egr-u-mn-hz-01 exited on signal 11 (Segmentation fault).

can anyone explain why?

DavidC | Wed, 11/09/2022 - 17:25

Hi!

I am new using the superquadrics library in liggghts, and I am trying to read a data file that contains some particles. However, I haven't had any success, it looks like I have also to read information on the superquadrics like shape and blockness. I went through the read_files.cpp and read_files.h, and no one of them shows any information about reading data when using superquadrics. Have you fixed the problem you mention above by any chance?

Thank you for your help in advance

Best,
David

deepakpawar.2310 | Mon, 03/07/2022 - 09:39

Hi

i think you need to define the particle template in the following way (by specifying semi axis parameters in x, y z direction with blockiness proprieties)
see the following the just an example

fix pts1 all particletemplate/superquadric 15485863 atom_type 2 density constant 2500 shape constant 0.00025 0.00025 0.0005 blockiness constant 2 2
fix pdd1 all particledistribution/discrete 86028157 1 pts1 1

hope it might helpful for you !!
Thank you

aks12 | Wed, 11/30/2022 - 06:35

Hello
After simulating superquadric particles, I am using Paraview 5.10.1 to visualize superquadric particles but it is showing spherical particles.
Can anyone explain the steps to visualize superquadric particles in paraview?
If any filter is needed can anyone send me to my following email id : dar1921.info@gmail.com
Thanks

aks12 | Thu, 12/01/2022 - 07:13

The process it is showing to follow is
1) Load plugins - can be auto-loaded next time

Tools - Manage Plugins - Load New - LiggghtsSuperquadricVTK.xml Tools - Manage Plugins - Load New - LiggghtsSuperquadricDUMP.xml

But these two files are are not there in the above link.

Thanks

aks12 | Thu, 12/01/2022 - 08:22

LIGGGHTS (Version LIGGGHTS-PUBLIC 3.8.0, compiled 2021-10-08-10:19:55 by root, git commit unknown)
units si
atom_style superquadric
atom_modify map array
boundary f f f
newton off
communicate single vel yes
dimension 3
#processors 1 1 1

# Declare domain
region reg block -2 2 -2 2 0.0 2 units box

create_box 1 reg
Created orthogonal box = (-2 -2 0) to (2 2 2)
2 by 4 by 2 MPI processor grid

neighbor 0.0025 bin
neigh_modify delay 0

neigh_modify delay 0 every 1 check yes page 500000 one 50000
### Setup
# Material and interaction properties
fix m1 all property/global youngsModulus peratomtype 5.e6
fix m2 all property/global poissonsRatio peratomtype 0.5
fix m3 all property/global coefficientRestitution peratomtypepair 1 0.45
fix m4 all property/global coefficientFriction peratomtypepair 1 0.30
# Physics
pair_style gran model hertz tangential no_history surface superquadric
WARNING:
The contact model you specified is not located in any whitelist.
Because of this the model will be run in an unoptimized version (increasing runtime by up to 20%).
In order to optimize this model you have the following options:
(i) Run the genAutoExamplesWhitelist.sh script in your LIGGGHTS(R) source folder to automatically parse the input script
(ii) Add the model combination by hand to your style_contact_model_user.whitelist that can be found in your LIGGGHTS(R) source folder
If you perform one of the steps above LIGGGHTS(R) needs to be recompiled to generate the optimized code.

(../contact_models.h:364)
#pair_style gran model hertz tangential history
pair_coeff * *
timestep 0.00001
fix gravi all gravity 9.81 vector 0.0 0.0 -1.0

# Particle insertion
fix pts1 all particletemplate/superquadric 123457 atom_type 1 density constant 2500 shape constant 0.0025 0.0025 0.0035 blockiness 4.0 4.0
ERROR: Illegal fix particletemplate/superquadric command, not enough arguments (../fix_template_superquadric.cpp:352)

During particle insertion I am getting this error.
Anyone have idea how to fix it?

Daniel Queteschiner | Thu, 12/01/2022 - 09:26

There is an argument missing in your fix particletemplate/superquadric command (also missing in the example given in the documentation)
fix pts1 all particletemplate/superquadric 123457 atom_type 1 density constant 2500 shape constant 0.0025 0.0025 0.0035 blockiness constant 4.0 4.0
cf. example case in our LIGGGHTS version
https://github.com/ParticulateFlow/LIGGGHTS-PFM/blob/master/examples/LIG...

atul2018 | Wed, 12/07/2022 - 11:46

just to clarify: superquadric particles are available for LIGGGHTS-Public and CFDEM-coupling and one can use this partilce type without any problem, am I right?

If yes, then do I have to restall my whole package with pulling new sourcefiles or it should be automatically updated in alreday installed CFDEM-coupling package.

Best Regards
Atul