problem about hybrid granular sph

Submitted by aaaachenjian on Mon, 09/21/2015 - 13:25

Dear LIGGGHTS team,
I'd like to do a simulation which hybrid the granular and sph atom styles
some granular particles in the bottom of a container, then add some water(sph model) on these particles, then close the lid.
My code is as follows

#### initialization #
#variables
variable mass universe 0.001 #0.001
variable h universe 0.012 #0.012

variable lat equal $h/1.2 # = 0.01
variable lathalf equal ${lat}*0.5
variable skin equal $h*0.25
variable wallpos equal ${lathalf}
variable eta equal 0.01*$h*$h

variable d equal 0.0108
variable r equal $d/2

units si
atom_style hybrid granular sph #
atom_modify map array sort 0 0.0 #...
boundary f f f
newton off
communicate single vel yes

region domain cylinder z 0. 0. 0.15 -0.20 0.30 units box
create_box 2 domain

#neighbor ${skin} bin
neigh_modify delay 0 check no

# setup #

fix cad all mesh/surface file cell.stl type 1 rotate axis 1. 0. 0. angle 90
fix cad2 all mesh/surface file lid.stl type 1 rotate axis 1. 0. 0. angle 90 move 0.001 0. 0.016

fix geometry all wall/gran model hertz tangential history mesh n_meshes 2 meshes cad cad2
fix wall2 all wall/gran model hertz tangential history primitive type 1 zcylinder 0.070 0. 0.

#fix pts all particletemplate/sphere 1 atom_type 1 density constant 1433 radius constant $r
#fix pdd all particledistribution/discrete 63243 1 pts 1.0

#region factory cylinder y 0. 0. 0.065 0.1 0.16 units box

region factory cylinder z 0 0 0.065 0.0 0.12 units box
#fix ins all insert/pack seed 20348 distributiontemplate pdd insert_every once overlapcheck yes maxattempt 100 all_in yes particles_in_region 1285 region factory ntry_mc 5000 #mass_in_region 1.2

lattice bcc ${lat}

fix wall all wall/sph zplane 0.14 NULL ${lathalf} 1.0

region water cylinder z 0. 0. 0.01 0.14 0.15 units box #0.17 0.186
create_atoms 2 region water
mass * ${mass}

lattice sc 0.011
create_atoms 1 region factory
mass 1 0.014
set atom 1 diameter $d

group particle type 1
group fluid type 2

fix m1 particle property/global youngsModulus peratomtype 2.e9 5.e5
fix m2 particle property/global poissonsRatio peratomtype 0.3 0.7
fix m3 particle property/global coefficientRestitution peratomtypepair 2 0.3 0.01&
0.01 0.005
fix m4 particle property/global coefficientFriction peratomtypepair 2 0.15 0.01 &
0.01 0.004

fix p1 fluid property/global speedOfSound peratomtype 10. 10.
fix p2 fluid property/global sl peratomtype $h $h
fix p3 fluid property/global artViscAlpha peratomtype 2.0833e-3 2.0833e-3
fix p4 fluid property/global artViscBeta peratomtype 0. 0.
fix p5 fluid property/global artViscEta scalar ${eta}
fix p6 fluid property/global tensCorrEpsilon scalar 0.2
fix p7 fluid property/global tensCorrDeltaP peratomtype ${lat} ${lat}

#sph pair style
# mhu = 1e-3 (water) ~ alpha * cAB * h
# for c=10 (10*vMax) and h=0.012 --> alpha=0.00208333
# pair_style sph kernel_style h [artVisc alpha beta cAB eta] [tensCorr epsilon]
# artifical viscosity [Monaghan and Gingold (1983)] and tensile correction [Monaghan (2000)]

pair_style hybrid gran model hertz tangential history sph/artVisc/tensCorr cubicspline $h artVisc tensCorr # 4.1666e-3 0. ${cAB} ${eta} 0.2

pair_coeff 1 1 gran
pair_coeff * 2 sph/artVisc/tensCorr

#sph fixes
# density
fix density fluid sph/density/continuity
fix corr fluid sph/density/corr shepard every 30
set group fluid meso_rho 1000

# pressure
# fix id group style type [if Tait: B rho0 gamma] (according to Monaghan 1994)
# B = c^2*rho0/gamma
# for c=10 --> B~15000
fix pressure fluid sph/pressure Tait 15000. 1000. 7.

fix integr fluid nve/sph
fix integrate particle nve/sphere
fix grav all gravity 9.81 vector 0. 0.0 -1.0

set group fluid sphkernel cubicspline

thermo_style custom step atoms ke cpu
thermo 10000
thermo_modify norm no lost ignore flush yes

timestep 5e-6

#fix ctg all check/timestep/gran 1 0.01 0.01
#run 1
#unfix ctg

dump dumpstl all stl 1000 post/dump*.stl
dump dmp_flu fluid custom 1000 post/wat*.liggghts id type type x y z ix iy iz vx vy vz fx fy fz radius p p rho
dump dmp_par particle custom 1000 post/par*.liggghts id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius

run 5000

unfix wall

fix pack all move/mesh mesh cad2 linear 0.0 0.0 -1.0
run 10400

unfix pack

But, when I ran it, I got the errors:

[[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ess_singleton_module.c at line 231
[[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ess_singleton_module.c at line 140
[[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file runtime/orte_init.c at line 128

I check the source file, but I can't understand the code. It seems to protect Windows OS.
I use tried version 3.1 and 3.2.1. Both of them show the same error.

Could some give me a favor?
Thanks!

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ckloss's picture

ckloss | Thu, 09/24/2015 - 09:46

Hi,

the error you are seeing does not have anything to do with LIGGGHTS, but with your system configuration and compilation of LIGGGHTS.

By the way - hybrid granular - sph is just not implemented. You'd have to implement it

Christoph

sstaple | Mon, 05/16/2016 - 21:54

Has anyone implemented this yet?????? I'd like this in there, but I wanted to check if anyone has done it before I break into this myself....