Having trouble with the very first tutorial example - Bin Flow

Submitted by Johan_Peter on Mon, 08/06/2018 - 16:08

We have downloaded the LIGGGHTS in our Linux server and getting the following error when we run
liggghts < binflow

********************************
sund30353.sund.root.ku.dk.23750hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
LIGGGHTS (Version LIGGGHTS-PUBLIC 3.8.0, compiled 2018-07-17-17:14:17 by xvt721, git commit 28301df8853491784b1d8b90533ea89b8c6af1e8)
Created orthogonal box = (-0.138 -0.138 -0.0045) to (0.138 0.138 0.43)
1 by 1 by 1 MPI processor grid
ERROR: Fix property/global (id m4): the number of default values must be a multiple of nCols. (../fix_property_global.cpp:129)
*******************************

Please advice what is wrong and what needs to be done.

Thank you

jsams | Tue, 08/07/2018 - 02:16

The binflow tutorial uses two different material types (atomtypes), i.e. one for the bin and one for the particles. This means that you need to define two material property values for each peratomtype property (e.g. young's modulus, poisson's ration, etv.) and four values for each peratomtypepair property (e.g. coefficient of restitution, friction coefficient, etc.) represented in a symmetric matrix.

See m4 in the tutorial:
fix m4 all property/global coefficientFriction peratomtypepair 2 0.2 0.175 0.175 0.5

Note the number of atom types (i.e. 2) after the peratomtypepair keyword and the identical values of 0.175 for positions 12 and 21 in the matrix, respectively.

The encountered error usually means that the number of values does not match the required number of values. Make sure that you provide the necessary values and that you don't no import any line breaks that could mess up the interpretation of the input.

Johan_Peter | Tue, 08/07/2018 - 10:51

Dear jsams

Thank you very much for your suggestion. We fixed a linebrak issue and this seems to have resolved that specific issue. We have subsequently now encountered another issue with the random number generator or the MPI.

******************************************
# Particle insertion
fix pts all particletemplate/sphere 1 atom_type 1 density constant 1000
ERROR on proc 0: Random number generation: It is required that the rando
a prime number.
The random seed used was 1
Hint 1: start with 'liggghts -echo both < in.script' to find out which
Hint 2: possible valid seeds would be the following numbers:
15485863, 15485867, 32452843, 32452867, 49979687, 49979693, 67
86028157 (../random.cpp:93)
------------------------------------------------------------------------
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.
------------------------------------------------------------------------

******************************************************

Is there a way to resolve this?

RAJ KASHYAP's picture

RAJ KASHYAP | Tue, 08/07/2018 - 14:00

Change the number according to prime number

for example fix pdd1 all particledistribution/discrete 15485863 1 pts1 1

where ever the seed number required provide it with prime number

Thanks

Raj Kashyap

mikejaeger | Thu, 03/28/2019 - 10:58

Hi People,

I am completely new to LIGGGHTS and I want to run the tutorial binflow. I have the same error message as above:

******************************************
# Particle insertion
fix pts all particletemplate/sphere 1 atom_type 1 density constant 1000
ERROR on proc 0: Random number generation: It is required that the rando
a prime number.
The random seed used was 1
Hint 1: start with 'liggghts -echo both < in.script' to find out which
Hint 2: possible valid seeds would be the following numbers:
15485863, 15485867, 32452843, 32452867, 49979687, 49979693, 67
86028157 (../random.cpp:93)
------------------------------------------------------------------------
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.
------------------------------------------------------------------------

******************************************************

I studied the whole forum here and made some changes to the code in the "partivel Insertion"-section.

fix pts all particletemplate/sphere 15485863 atom_type 1 density constant 1000 & # before there was 1 instead of 15485863
radius constant 0.0015
fix pdd all particledistribution/discrete 15485863 1 pts 1.0 # before there was 63243 instead of 15485863
region factory cylinder z 0 0 0.10 0.4 0.41 units box
fix ins all insert/rate/region seed 15485863 distributiontemplate pdd & # before there was 123481 instead of 15485863
nparticles 150000 particlerate 150000 insert_every 1000 &
overlapcheck yes vel constant 0. 0. -1.0 region factory ntry_mc 10000

And then a next error-message occurs. I tried so many times with other examples, but this error message is not eliminatable.

LIGGGHTS (Version LIGGGHTS-PUBLIC 3.8.0, compiled 2019-03-27-12:56:42 by mikejaeger, git commit ce1931e377a2945e3fa25dae0eebc1f697009a32)
Created orthogonal box = (-0.138 -0.138 -0.0045) to (0.138 0.138 0.43)
1 by 2 by 2 MPI processor grid
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%
ERROR on proc 0: Fix insert/rate/region, ID ins: Random number generation: It is required that all the random seeds of this fix insert/*,
the random seed of particle distribution fix (id pdd) template and all random seeds of the
fix particletemplate/* commands used by particle distribution fix (id pdd) are different
Hint: possible valid (different) seeds would be the following numbers:
15485863, 15485867, 32452843, 32452867, 49979687, 49979693, 67867967, 67867979, 86028121, 86028157 (../fix_insert.cpp:475)
--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------

SIGINT/SIGTERM caught - Writing restart on next occasion and quitting after that.

SIGINT/SIGTERM caught - Writing restart on next occasion and quitting after that.

SIGINT/SIGTERM caught - Writing restart on next occasion and quitting after that.

My whole code is:

### 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

# 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 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 15485863 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 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
fix integrate all nve/sphere

# Gravity
fix grav all gravity 9.81 vector 0.0 0.0 -1.0

# Time step
timestep 0.00001

# Thermodynamic output settings
thermo_style custom step atoms ke cpu
thermo 10000
thermo_modify norm no lost ignore

# Check time step and initialize dump file
fix ctg all check/timestep/gran 1 0.01 0.01
run 1
unfix ctg

# Create imaging information
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

### Execution and further settings
# Fill the hopper
run 150000 upto

# Pull the stopper
unfix stopper

run 300000

Someone knows the solution? It would be so great! I installed LIGGGHTS-PUBLIC yesterday on my Ubuntu 18.10., with the Installation guide. (Just execute "make auto" and the LIGGGHTS-PUBLIC was installed).

mikejaeger | Fri, 03/29/2019 - 18:31

Thank you very much! It worked! Now it's calculating and several *.stl files are generated. When I want to open them in paraview I only the ther geometry of the hopper.stl and no spheres.
I recognized that there is one huge file "dump.1" (I think this is the particle data) but this file is not readable with paraview. How can I make this readable for paraview?

Thank you in advance!