ABOUT: gran/hooke/history/stiffness

Submitted by venes520 on Thu, 03/01/2012 - 08:48

Hi,
Does anyone is now using the gran/hooke/history/stiffness command?
I am using it but system warned:
[localhost:13166] *** Process received signal ***
[localhost:13166] Signal: Segmentation fault (11)
[localhost:13166] Signal code: Invalid permissions (2)
[localhost:13166] Failing at address: 0x7fc06aa59000
[localhost:13166] [ 0] /lib64/libpthread.so.0(+0xf500) [0x7fc06fe13500]
[localhost:13166] [ 1] liggghts() [0x51681c]
[localhost:13166] [ 2] liggghts() [0x59761b]
[localhost:13166] [ 3] liggghts() [0x4fe93b]
[localhost:13166] [ 4] liggghts() [0x426a34]
[localhost:13166] [ 5] liggghts() [0x42739c]
[localhost:13166] [ 6] liggghts() [0x4be902]
[localhost:13166] [ 7] /lib64/libc.so.6(__libc_start_main+0xed) [0x7fc06fa6d69d]
[localhost:13166] [ 8] liggghts() [0x409929]
[localhost:13166] *** End of error message ***

Does it relate to this gran/hooke/history/stiffness command?
Also, anyone can suggest an effective way to select binsize?
Thanks very much !!

Below is my script, please take a look

# LIGGGHTS version: 1-5-1

# Direct shear box test

# Based on Xuetao Tong's script

units si

atom_style granular

atom_modify map array

boundary f f f

newton off

# Read data

region reg block -2.0 2.0 -2.0 2.0 -2.0 2.0 units box

create_box 3 reg

communicate single vel yes

neighbor 0.003 bin

neigh_modify delay 0

#=============Material properties required for new pair style===================

fix normal all property/global kn peratomtypepair 3 0 9.0e5 9.0e5 &

9.0e5 5.0e5 9.0e5 &

9.0e5 9.0e5 0

fix tangent all property/global kt peratomtypepair 3 0 0 0 &

0 1.5e4 0 &

0 0 0

fix damping_n all property/global gamman_abs peratomtypepair 3 0 0 0 &

0 5.56e-2 0 &

0 0 0

fix damping_t all property/global gammat_abs peratomtypepair 3 0 0 0 &

0 0.99e-2 0 &

0 0 0

fix coeff_friction all property/global coefficientFriction peratomtypepair 3 0 0 0 &

0 0.3 0 &

0 0 0

# type 1 : wall of boxes

# type 2 : filled particles

# type 3 : pariticle-wall

#=============Define pair style===================

pair_style gran/hooke/history/stiffness 1 0 #Hookean without cohesion

pair_coeff * *

timestep 0.000001

#granular walls

fix upperbox all mesh/gran/stressanalysis uppernew.stl 1 0.001 0. 0. 0. 0. 0. 0.

fix lowerbox all mesh/gran/stressanalysis lower.stl 1 0.001 0. 0. 0. 0. 0. 0.

fix cover all mesh/gran/stressanalysis cover.stl 1 0.001 0. 0. 0. 0. 0. 0.

fix container all wall/gran/hooke/history/stiffness 1 0 mesh/gran 3 upperbox lowerbox cover

#define particles insertion into domain

fix pts1 all particletemplate/sphere 1 atom_type 2 density constant 2000 radius constant 0.0028

fix pdd1 all particledistribution/discrete 1 1 pts1 1

#============diamter of particles: 4 mm==============

#============region and insertion===================

region upper block 0.0 0.05 0.0 0.03 0.0 0.02 units box

region lower block 0.0 0.05 -0.03 0.0 0.0 0.02 units box

group upper region upper

group lower region lower

group total union upper lower

fix ins_upper total pour/dev/packing 1 distributiontemplate pdd1 &

vol 0.6 100 region upper #overlapcheck no

fix ins_lower total pour/dev/packing 1 distributiontemplate pdd1 &

vol 0.6 100 region lower #overlapcheck no

fix gravi all gravity 9.81 vector 0.0 -1.0 0.0

#=========apply nve integration to all particles that are inserted as single particles==========

fix NVE_integration total nve/sphere

dump I_stl all mesh/gran/VTK 100000 Stress_file-*.vtk stress stresscomponents

#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

#=============insert the first particles so that dump is not empty=============

run 1

dump dmp all custom 100000 dump.v_4_1 id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius

run 1000000

unfix ins_upper

unfix ins_lower

run 200000

#=============wiggle, sample preparation==============

fix wigglecylin1 all move/mesh/gran wiggle -0.004 0 0 0.05 upperbox

fix wigglecylin2 all move/mesh/gran wiggle -0.004 0 0 0.05 lowerbox

fix wigglecylin3 all move/mesh/gran wiggle -0.004 0 0 0.05 cover

run 400000

unfix wigglecylin1

unfix wigglecylin2

unfix wigglecylin3

run 100000

#=============unfix cover============

unfix cover

unfix container

fix container_new all wall/gran/hooke/history/stiffness 1 0 mesh/gran 2 upperbox lowerbox

#=============create particle-wall & add force===========

#creat particle-wall N = 1.665 kN

region pwall_region block 0.005 0.045 0.035 0.045 0.005 0.015 units box

lattice custom 0.005 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0.5 0.5 0.5

create_atoms 3 region pwall_region

group pwall region pwall_region

set group pwall diameter 0.005 density 5000

fix set_rigid all rigid group 1 pwall torque * off off off

neigh_modify exclude type 3 3

# apply confining pressure

fix addforce pwall aveforce 0.0 -15 0.0

fix shear all move/mesh/gran linear 0.1 0 0 units box lowerbox 1

run 400000

venes520 | Fri, 03/02/2012 - 17:57

Dear Christoph

Sorry for that and sorry for the emails, I was a bit desperate..
Attached please find the log file, input script and stl. files. (attached to the original post)

Please note that the log file is not the very original one because I make minor changes on the bin value and particles size. But the all generate the same kind of warnings: segmentation fault.
Sometime when I changed the bin value and particle size, it warned "too many atom sorting bins" or "Failed to allocate ..bytes to ..."
For the "segmentation fault", the log file didn't record anything as I guess it was interrupted. But LIGGGHTS did print out the "segmentation fault" warning on the screen as posted above.

A kind forum member has just run the script for me on parallel computers, my script worked just fine. As he switched to single computer, the script didn't work either......(I might be able to post his dump file tomorrow)

Please take a look. I don'[t think my script needs to run on parallel computers (just a few particles) and it's a bit hard for me to set up that.
Thanks in advance.

Cheers
Anson Liang