LIGGGHTS tutorial

That is absolutely helpful:) Thank you Chris!

This is very well done and has a lot of very helpful information for newcomers to the code. If I had this a year ago I would have been in heaven.

kudos!

jon

Hi Chris,

This is really good job. Could you please give a link of the primitive Mesh for Example 2 – Continuous Blending Mixer?

thanks

David Long

Thanks for posting this. Very useful.

This is really helpful! Really appreciate your work. Are those stl files in the examples available for us to try?

Thanks a lot,

Cheng

Hi Chris,

Thank you so much for responding my comment so quickly. I'm still new to LIGGGHTS and trying to run the CB Mixer #1 example.

Here is the error I got from my run.
-------------------------------------------------------------------
LAM 7.1.2/MPI 2 C++/ROMIO - Indiana University

Adding fix balance
Adding fix balance
Adding fix balance
Adding fix balance
Adding fix balance
Adding fix balance
Adding fix balance
LIGGGHTS (Version LIGGGHTS-PUBLIC 2.3.6, compiled 2013-07-12-11:47:58 by huangc based on LAMMPS 20 Apr 2012)
Created orthogonal box = (-0.32 -1.96 -0.29) to (0.32 1.46 0.335)
1 by 8 by 1 MPI processor grid

Reading STL file 'trough2.stl'

Reading STL file 'left_shaft2.stl'

Reading STL file 'right_shaft2.stl'
Fix particledistribution/discrete (id pdd): distribution based on mass%:
pts: d=1.000000e-02 (max. bounding sphere) mass%=100.000000%
Fix particledistribution/discrete (id pdd): distribution based on number%:
pts: d=1.000000e-02 (max. bounding sphere) number%=100.000000%
Setting up run ...
Mesh cad1: 785 elements have high aspect ratio (angle < 0.500000 °)
WARNING: Fix mesh: Mesh contains highly skewed element, moving mesh (if used) will not parallelize well (surface_mesh_I.h:485)
Import and parallelization of mesh cad1 containing 3320 triangle(s) successful
Mesh cad2: 1264 elements have high aspect ratio (angle < 0.500000 °)
WARNING: Fix mesh: Mesh contains highly skewed element, moving mesh (if used) will not parallelize well (surface_mesh_I.h:485)
Import and parallelization of mesh cad2 containing 18308 triangle(s) successful
Mesh cad3: 1158 elements have high aspect ratio (angle < 0.500000 °)
WARNING: Fix mesh: Mesh contains highly skewed element, moving mesh (if used) will not parallelize well (surface_mesh_I.h:485)
Import and parallelization of mesh cad3 containing 18650 triangle(s) successful
INFO: Resetting random generator for region factory
INFO: Particle insertion ins: 99.471840 particles every 1000 steps - particle rate 3183.098868 (mass rate 1.666667)
10000000 particles (mass 5235.987756) within 100530964 steps
Memory usage per processor = 16.1654 Mbytes
Step Atoms KinEng CPU
0 0 -0 0
INFO: Particle insertion ins: inserted 99 particle templates (mass 0.051836) at step 1
- a total of 99 particle templates (mass 0.051836) inserted so far.
WARNING: time-step is 18.250596 % of rayleigh time
WARNING: time-step is 5.484682 % of hertz time
1 99 0.025926086 0.037512779
Loop time of 0.0375237 on 8 procs for 1 steps with 99 atoms

Pair time (%) = 3.18885e-06 (0.00849821)
Neigh time (%) = 0.00258887 (6.89928)
Comm time (%) = 2.18153e-05 (0.0581373)
Outpt time (%) = 3.67463e-05 (0.097928)
Other time (%) = 0.0348731 (92.9362)

Nlocal: 12.375 ave 58 max 0 min
Histogram: 6 0 0 0 0 0 0 1 0 1
Nghost: 0.625 ave 4 max 0 min
Histogram: 6 0 1 0 0 0 0 0 0 1
Neighs: 0.25 ave 2 max 0 min
Histogram: 7 0 0 0 0 0 0 0 0 1

Total # of neighbors = 2
Ave neighs/atom = 0.020202
Neighbor list builds = 1
Dangerous builds = 0
Adding fix balance
ERROR: Invalid fix style (modify.cpp:724)

LAM 7.1.2/MPI 2 C++/ROMIO - Indiana University
---------------------------------------------------------------------

Here are last two lines in the log.liggghts file:
------------------------------------------------------------------------------
fix lb all balance 0 xyz 10 1.1 out balance.txt
ERROR: Invalid fix style (modify.cpp:724)
------------------------------------------------------------------------------
I guess that I'm missing the balance.txt file.

Thanks again for your help,

Cheng

Sorry, I read the doc file about this 'fix balance' command
----------------------------
fix lb all balance 0 xyz 10 1.1 out balance.txt
----------------------------
The balance.txt is the output file name.
When I disabled this line, I can run the simulation.
I copied and pasted the input file for CB Mixer #1 simulation from the Benchmarking Study pdf file.

Thanks,

Cheng

Hi to all
i can't found the CAD archive of the examples.
Please, how i do it?, some link with the folder?

i will be very grateful
Thanks for the answers

i'm sorry,
i'm confused with the extension.
My final problem is with the download, extension .bin
i don't know how decompress this format

Forget it
i did it

Thank you Chris

Hi Chris,

I am unable to download the zipped file. When I try to download it, it only shows as if a part of the file will be downloaded and when trying to extract, it says internal error.
I guess it has to do with the forum. Any other possibility to download those files?

Thanks,
Sam

Hi guys,

I have a problem to import mesh from cad,
I follow step to step this tutorial, example #1 and i can't import file hopper.stl
In the terminal appears this:
fix cad1 all mesh/surface file hopper.stl type 2 scale 0.0001
ERROR on proc 0: Cannot open mesh file hopper.stl (input_mesh_tri.cpp:78)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

Somebody know what happened?
Thank you again

Anybody can help me?

Is hopper.stl in your current folder?

Yes AGI i do it and liggghts the read it.
i have a one question more, how to see the results en paraview, with a command?

Hi Chris,

i am trying to get some practice working with LIGGGHTS and try to get your tutorials run.
Recently i wanted to simulate the binFlow case but i get an error telling "invalid fix style: "wall/gran/hertz/history"

Here is the log file:

LIGGGHTS (Version LIGGGHTS-PUBLIC 3.0.0, compiled 2014-03-06-15:35:14 by dorn based on LAMMPS 23 Nov 2013)
### Bin Flow Simulation
###
###
###
###
###
#This simulation involves inserting a set of particles into a cylindrical hopper,
#allowing them to settle under gravity, and then suddenly opening a stopper at the
#bottom of the hopper and allowing the particles to pour out. We track the
#flowrate of material from the hopper by tracking how many particles remain in the
#system as a function of time.

### Initialization
# Preliminaries
units si
atom_style sphere
atom_modify map array
boundary f f f
newton off
communicate single vel yes
#processors 2 2 3

# Declare domain
region domain block -0.138 0.138 -0.138 0.138 -0.0045 0.43 units box
create_box 2 domain
Created orthogonal box = (-0.138 -0.138 -0.0045) to (0.138 0.138 0.43)
1 by 1 by 1 MPI processor grid

# Neighbor listing
neighbor 0.003 bin
neigh_modify every 1 check no

### Setup
# Material and interaction properties required
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

# Particle insertion
fix pts all particletemplate/sphere 1 atom_type 1 density constant 1000 radius constant 0.0015
fix pdd all particledistribution/discrete 63243 1 pts 1.0
region factory cylinder z 0 0 0.10 0.4 0.41 units box
fix ins all insert/rate/region seed 123481 distributiontemplate pdd nparticles 150000 particlerate 150000 insert_every 1000 overlapcheck yes vel constant 0. 0. -1.0 region factory ntry_mc 10000

# Import mesh from cad:
fix cad1 all mesh/surface file hopper.stl type 2 scale 0.001

# Use the imported mesh as granular wall
fix geometry all wall/gran/hertz/history mesh n_meshes 1 meshes cad1
ERROR: Invalid fix style: " wall/gran/hertz/history " (../modify.cpp:793)

Thanks a lot for help!

Best,
martin

Hi Martin,

I suppose your problem is due to a syntax error. As far as I know, the way walls are defined changed with LIGGGHTS 3.0.
You should be able to figure out the correct syntax by having a look at the documentation for fix wall.

Best regards,
MiRa

Hi MiRa,

yeah that also was my thought. The problem is based on the new version 3.0.0. the syntax has changed.
For all interested in that problem:

example (manual page 688):
OLD: fix ID group-ID wall/gran/hertz/history mesh n_meshes 2 meshes cad1 cad2
NEW: fix ID group-ID wall/gran model hertz tangential history mesh n_meshes 2 meshes cad1 cad2

Thanks!

Bests,
martin

Hello i've got a problem and i really need some help. here is the point: i took one of example scripts and made some changes, i,ve tryed to run it but is stopped on the line "run1" maybe somebad knows how to beat it? i mean i searched whole forum but i have not got anything...
Here is my code and it would be great if somebody tell me where i was wrong

### Initialization

# Preliminaries

atom_style granular
atom_modify map array
boundary f f f
newton off

communicate single vel yes

units si

# Declare domain
region reg block -0.9 0.9 -0.9 0.9 -0.2 0.5 units box
create_box 1 reg

neighbor 0.002 bin
neigh_modify delay 0

# Material and interaction properties required
fix m1 all property/global youngsModulus peratomtype 4e10
fix m2 all property/global poissonsRatio peratomtype 0.13
fix m3 all property/global coefficientRestitution peratomtypepair 1 0.65
fix m4 all property/global coefficientFriction peratomtypepair 1 0.46
fix m5 all property/global coefficientRollingFriction peratomtypepair 1 0.1
fix m6 all property/global k_finnie peratomtypepair 1 1.0

#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

#the mill
fix cad1 all mesh/surface/stress file meshes/rotor.stl type 1 wear finnie
fix cad2 all mesh/surface/stress file meshes/stator.stl type 1 wear finnie
fix inface all mesh/surface file meshes/insertion_face.stl type 1
fix granwalls all wall/gran model hertz tangential history mesh n_meshes 2 meshes cad1 cad2

#distributions for in
fix pts1 all particletemplate/sphere 1 atom_type 1 density constant 2500 radius constant 0.0012
fix pts2 all particletemplate/sphere 1 atom_type 1 density constant 2500 radius constant 0.0025
fix pdd1 all particledistribution/discrete 1. 2 pts1 0.3 pts2 0.7

#region and insertion
group nve_group region reg
region bc cylinder z 0.0 0.0 0.1 0.240 0.5 units box

#particle insertion
fix ins nve_group insert/stream seed 5330 distributiontemplate pdd1 &
nparticles 6000 massrate 0.1 insert_every 100000 overlapcheck yes all_in no vel constant 0.0 0.0 -1.0 &
insertion_face inface

#apply nve integration to all particles that are inserted as single particles
fix integr nve_group nve/sphere

#output settings, include total thermal energy
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes

#rotate the shafts
fix movecad1 all move/mesh mesh cad1 rotate origin 0. 0. 0. &
axis 0. 0. -1 period 0.036 # 1650 RPM

#insert the first particles so that dump is not empty
run 1
dump dmp all custom 200 post/dump*.chute id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius
dump dumpstress all mesh/gran/VTK 200 post/dump*.vtk stress wear cad1 cad2

#insert particles
run 100000 upto
unfix ins

Thanks Chris

This needs to be updated to reflect the changes in the latest version of LIGGGHTS. Many of the examples no longer work and it's impossible for someone starting out with LIGGGHTS to find what has changed as the documentation is such a hash-up of LAMMPS references. Incredibly annoying and wasted many hours of time

JP

Hi JP,

yes - you are right! After you found out what needs to be updated, would you be willing to contribute and do these changes? Just send me a PM

Christoph

Hi,
I'm using liggghts 2.3.8, I checked net but I can't find any user manual for this version.
Could anyone help me?
Regards,
Reza

Hi Reza,

do not use an old version - 2.3.8 is no longer supported. Please always update to the latest and greatest!

Christoph

Hi All,

1- Is the ellipsoid atom_style invalid for granular model?
2- Could you please give an easy way to create meshes?
3- Could you please include an example of ellipsoid and line atom_style in example folder?
4- Could you please include a PDF version of tutorials?

Best regards,
Reza

Hey thanks so much for this great tutorial. I am attempting to run the binflow tutorial and it keeps giving me an error that I don't know how to fix. The output from the command
liggghts -echo both < in.bin

# Particle insertion
fix pts all particletemplate/sphere 1 atom_type 1 density constant 1000 radius constant 0.0015
ERROR on proc 0: Random number generation: It is required that the random seed value is > 10000 and a prime number.
The random seed used was 1
Hint 1: start with 'liggghts -echo both < in.script' to find out which command caused this
Hint 2: possible valid seeds would be the following numbers:
15485863, 15485867, 32452843, 32452867, 49979687, 49979693, 67867967, 67867979, 86028121, 86028157 (../random.cpp:69)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

Any help on this issue would be greatly appreciated.

Hi jordantcox,

with the new release 3.5 it is necessary to set the seed number > 10000 and as a prime number.
I am sure there is a meaningful reason for it :D

So like LIGGGHTS gives you several numbers as examples. (15485863, 15485867, 32452843, 32452867, 49979687, 49979693, 67867967, 67867979, 86028121, 86028157 )
When you change fix pts all particletemplate/sphere 1 atom_type 1 density constant 1000 radius constant 0.0015 to fix pts all particletemplate/sphere 15485863 atom_type 1 density constant 1000 radius constant 0.0015 it should be fine.

Regards,
Westbrink

Hey Westbrink,

It has been a couple of weeks and I am still trying on this. I have updated the particle insertion section to read as follows, and I get the same error as before but now it is for a different line.

# Particle Insertion
fix pts all particletemplate/sphere 15485863 atom_type 1 density constant 1000 &
radius constant 0.0015
fix pdd all particledistribution/discrete 15485863 1 pts 1.0
region factory cylinder z 0 0 0.10 0.4 0.41 units box
fix ins all insert/rate/region seed 123481 distributiontemplate pdd &
nparticles 150000 particlerate 150000 insert_every 1000 &
overlapcheck yes vel constant 0. 0. -1.0 region factory ntry_mc 10000

Any help would be great.

Thanks,
Jordan

Hey thanks again for the comments. After reading some manuals I was able to fix it.

Thanks,
jordan

Hello
I installed the program, I'm running the example 1 and 4 of the tutorial, but I get random numbers error, can you help me?
Thank you

Hi Luci,

You are not the first one to encounter this error in the tutorial cases (go to http://www.cfdem.com/forums/bin-flow-tutorial for help).

Advice for the future: If you encounter any further problems in your simulations, the forum provides a search function where you can see if anyone has had similar problems before.

Hello everyone
I am having this error and I have not been able to solve it ... someone could help me

### Initialization
# Preliminaries
units si
atom_style sphere
atom_modify map array
boundary f f f
newton off
communicate single vel yes
#processors * * *
# Declare domain
region domain block -0.138 0.138 -0.138 0.138 -0.0045 0.43 units box
create_box 2 domain
Created orthogonal box = (-0.138 -0.138 -0.0045) to (0.138 0.138 0.43)
1 by 1 by 1 MPI processor grid
# Neighbor listing
neighbor 0.003 bin
neigh_modify every 1 check no

### Setup
#Material and interaction properties required
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
# Particle insertion
fix pts all particletemplate/sphere 15485863 atom_type 1 density constant 1000 radius constant 0.0015
fix pdd all particledistribution/discrete 15485867 1 pts 1.0
Fix particledistribution/discrete (id pdd): distribution based on mass%:
pts: d=3.000000e-03 (max. bounding sphere) mass%=100.000000%
Fix particledistribution/discrete (id pdd): distribution based on number%:
pts: d=3.000000e-03 (max. bounding sphere) number%=100.000000%
region factory cylinder z 0 0 0.10 0.4 0.41 units box
fix ins all insert/rate/region seed 32452843 distributiontemplate pdd nparticles 150000 particlerate 150000 insert_every 1000 overlapcheck yes vel constant 0. 0. -1.0 region factory ntry_mc 10000

# Import mesh from cad:
fix cad1 all mesh/surface file hopper.stl type 2 scale 0.001

Reading STL file 'hopper.stl' (mesh processing step 1/3)
# Use the imported mesh as granular wall
fix geometry all wall/gran model hertz tangential history mesh n_meshes 1 meshes cad1
# Create stopper for funnel
fix stopper all wall/gran model hertz tangential history primitive type 2 zplane 0.0
# Define the physics
pair_style gran model hertz tangential history
pair_coeff * *
### Detailed settings
Integrator
ERROR: Unknown command: Integrator (../input.cpp:258)

Integrator is not a liggghts command, I believe you want
fix integrator all nve/sphere
where
fix == liggghts command
integrator == id for this fix
all == you want to integrate "all" particles
nve/sphere == integrator particle's position, velocity, and angular velocity (http://www.cfdem.com/media/DEM/docu/fix_nve_sphere.html)

Under your ### Detailed Settings, there is the line Integrator. Integrator is not a command but I believe you want it there as a comment. Either make Integrator a comment or delete it.

While debuging your input file, it is often helpful for me to add -echo both to my command. This will print out what ligggghts is doing and allows you to see what line breaks the simulation.

$LIGGGHTS -echo both < in.simulation

Hi dear friends, I downloaded the tutorial, but the instruction is different for Workbench STARTER. For example I review the bin flow with hopper.

Best regards

Victor

Hi Chris,

I am running the shear cell but i get an below error and even i am understanding the meaning of this error. Can you please help me ?

ERROR: Fix wall/gran (id geometry): More than one wall of type 'mesh' is not supported