segmentation fault in easo/capillary/viscous

Submitted by NSalloum on Fri, 11/23/2018 - 11:37

hello,

I think there is some sort of a bug in the easo/capillary/viscous cohesive model whereI am trying to run a simulation introducing cohesive model, but I am getting the following error:

[salloum-VirtualBox:16626] *** Process received signal ***
[salloum-VirtualBox:16626] Signal: Segmentation fault (11)
[salloum-VirtualBox:16626] Signal code: Address not mapped (1)
[salloum-VirtualBox:16626] Failing at address: (nil)
[salloum-VirtualBox:16626] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7f7292e08890]
[salloum-VirtualBox:16626] [ 1] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x2c391d)[0x564ec0d9b91d]
[salloum-VirtualBox:16626] [ 2] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x31ce57)[0x564ec0df4e57]
[salloum-VirtualBox:16626] [ 3] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x1c57e8)[0x564ec0c9d7e8]
[salloum-VirtualBox:16626] [ 4] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x1c2126)[0x564ec0c9a126]
[salloum-VirtualBox:16626] [ 5] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x5f3fcb)[0x564ec10cbfcb]
[salloum-VirtualBox:16626] [ 6] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x6e138a)[0x564ec11b938a]
[salloum-VirtualBox:16626] [ 7] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x1383f0)[0x564ec0c103f0]
[salloum-VirtualBox:16626] [ 8] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x1a2ce5)[0x564ec0c7ace5]
[salloum-VirtualBox:16626] [ 9] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x1a0645)[0x564ec0c78645]
[salloum-VirtualBox:16626] [10] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0x1a0eee)[0x564ec0c78eee]
[salloum-VirtualBox:16626] [11] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0xb8a0c)[0x564ec0b90a0c]
[salloum-VirtualBox:16626] [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f7292a26b97]
[salloum-VirtualBox:16626] [13] /home/salloum/LIGGGHTS-BOSCH-master/src/lmp_auto(+0xba0ba)[0x564ec0b920ba]
[salloum-VirtualBox:16626] *** End of error message ***
###################################################################################################

The input script I am using is as follows:

###### Angle of Repose ######
#coarse graining application
coarsegraining 6.0 model_check warn
modify_timing verbose
### Initialization

# Preliminaries
########## Standard block #############
atom_style sphere
atom_modify map array
boundary f f f
newton off
communicate single vel yes
units si
######################################

# Simulation Domain
region domain block -0.05 0.05 -0.05 0.05 -0.086 0.2 units box
create_box 2 domain

# Neighbor listing
neighbor 0.0000155 bin #0.25xradius_max #particle diameter
neigh_modify delay 0

# Define Material propertiesf
fix m1 all property/global youngsModulus peratomtype 1.0e7 1.0e7
fix m2 all property/global poissonsRatio peratomtype 0.3 0.3
fix m3 all property/global coefficientRestitution peratomtypepair 2 0.6 0.3 0.3 0.3
fix m4 all property/global coefficientFriction peratomtypepair 2 0.61 0.115 0.115 0.1
fix m5 all property/global coefficientRollingFriction peratomtypepair 2 1.56 0.6 0.6 0.6

fix m6 all property/global minSeparationDistanceRatio scalar 1.01
fix m7 all property/global maxSeparationDistanceRatio scalar 1.1
fix m8 all property/global surfaceLiquidContentInitial scalar 0.1
fix m9 all property/global surfaceTension scalar 0.0728
fix m10 all property/global fluidViscosity scalar 0.00534
fix m11 all property/global contactAngle peratomtype 25 0

# Define contact model
pair_style gran model hertz tangential history cohesion easo/capillary/viscous rolling_friction epsd2
pair_coeff * *

# Time step
timestep 0.000005 #5e-6

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

# Import mesh from cad
fix cad1 all mesh/surface file meshes/meshed_face_Hopper_D5_1_extension.stl type 2 rotate axis 1 0 0 angle -90 move 0.0 0.0 38.01 scale 0.001

fix cad2 all mesh/surface file meshes/meshed_face_Container_1.stl type 2 rotate axis 1 0 0 angle 90 move 0.0 0.0 -80.0 scale 0.001

# Use the imported meshes as granular walls
fix geometry1 all wall/gran model hertz tangential history cohesion easo/capillary/viscous rolling_friction epsd2 mesh n_meshes 2 meshes cad1 cad2

#region of insertion
region factory cylinder z 0 0 0.03 0.066 0.067 units box

# Integrator
fix integrate all nve/sphere

# Create stopper for funnel
fix stopper all wall/gran model hertz tangential history cohesion easo/capillary/viscous rolling_friction epsd2 primitive type 2 zplane 0.0

# Particle insertion
fix pts1 all particletemplate/sphere 15485863 atom_type 1 density constant 1536.1 &
radius constant 0.000062

fix pdd all particledistribution/discrete 15485867 1 pts1 1.0

fix ins all insert/rate/region seed 32452843 distributiontemplate pdd &
mass 0.005 massrate 0.005 insert_every 1000 &
overlapcheck yes vel constant 0.0 0.0 -1.0 region factory ntry_mc 10000
#5g

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

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

# Create imaging information #make a dump of particles and the stl file
dump dmp all custom 20002 post/movingMesh_*.liggghts id type type mass x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius diameter
dump dumpstl all mesh/stl 20002 post/dump*.stl

### Execution and further settings

# Fill the hopper
run 400000 upto

# Pull the stopper
unfix stopper

run 800160

####################################################################################################

Please note that I added the used models to the whitelist file.

Any suggestions in this regards please?

best wishes

AttachmentSize
Binary Data cad.tar_.gz4.93 MB
Binary Data log.tar_.gz31.58 KB

paul | Sat, 11/24/2018 - 12:45

> fix m11 all property/global contactAngle peratomtype 25 0
Name one liquid that has a contact angle of 0 - try giving this a nonzero value.

NSalloum | Mon, 11/26/2018 - 04:51

hello Paul,
I already tried changing this before, but still giving me the same error,so:
-in what way should I think to overcome it ?
-would be a problem in the model itself?

best wishes,

lcraul | Mon, 05/06/2019 - 22:29

Hi, Mr. Arnom, have you solved this error? I have encountered the similar error and have no idea on how to deal with it. Do you have any suggestion?

NSalloum | Thu, 12/20/2018 - 08:46

hello Arnom,

Please find attached the stl files in the 1st post, but note that upon using the washino model having the same settings mentioned above, I got no segmentation error, but the particles are blowing up when they become in contact. Moreover, the percentage of Hertz time is exceeding the 10% after being started by around 6%, so what do you think the cause of this increase in velocity?

best wishes,

arnom's picture

arnom | Mon, 01/14/2019 - 13:24

Thank you, I can reproduce the segfault in my dev version. I will have a look at it over the next weeks.

DCS team member & LIGGGHTS(R) core developer

arnom's picture

arnom | Mon, 01/14/2019 - 13:50

Just one more small request. Could you please post the full log file that you get.

Thanks,
Arno

DCS team member & LIGGGHTS(R) core developer

NSalloum | Mon, 01/14/2019 - 16:26

Thanks Mr. Arnom,

Please find attached the log file in the 1st post also.

But may you please answer my second question regarding the blowing of the particles in the washino/capillary/viscous model as I am in hurry for using it.

best wishes,

lcraul | Mon, 05/06/2019 - 22:26

Hi, Nizar, have you solved this error? I have encountered the similar error and have no idea on how to deal with it. Do you have any suggestion?