some questions about installation on Ubuntu 14.04

Asked by Wang Yaqiong on 2020-10-21

My work is to establish model of different materials, and I make use of "wall-ball" and "ball-ball" bond interaction in my script.

Due to some bugs on my computer when I ran some scripts, I reinstalled ESyS-Particle2.3.2 on Ubuntu 14.04 according to this tutorial: https://answers.launchpad.net/esys-particle/+faq/1613 , but I found particles connected through bond interactions were not stable. The displacement in z and x direction is not zero even though I did not have any force, friction statement in my script ( in the script, I only created the particles that were bonded together without any other processing), and the e_kin is also not zero. But I do not have that problem before my reinstallation.

My question is:
1. Is there any problems with my installation according to that tutorial? (After my installation, I could successfully run the bingle_output.py)
2. Should I reinstall the latest version of ESyS-Particle.2.3.5 on Ubuntu14.04? Is that system compatible with the latest version?
3. If there is no problem with my installation, what could be the potential reason of that abnormal phenomenon?

Here is my script:
from esys.lsm import *
import math
from esys.lsm.util import *
from esys.lsm.geometry import *

#instantiate a simulation object and
#initialise the neighbour search algorithm:
sim = LsmMpi (numWorkerProcesses =1 , mpiDimList = [1,1,1])
sim.initNeighbourSearch (
 particleType = "RotSphere",
 gridSpacing = 0.002, #>=2.5*Rmax+0.2*Rmin
 verletDist = 0.00003 #>=0.2*Rmin
)

############################# constants parameters ##################################
alfa = 1e6
rhos = 910.0*alfa
dMu=0.37; sMu=dMu
kr=1.0; eta=0.10
beta=0.001

########################### geometry ##############################################
rMean0=0.00035
rmin = 0.00005
rmax=.0006 # xin Sat 17 Oct 2020 02:39:24 PM CST
R_GT=0.05e-3
R_GM=0.6e-3
######################## Shear Control #############################################
wallName = ["top_wall", "bottom_wall"]
meshName = ["left_mesh_wall", "right_mesh_wall"]
interactionName = ["top_repel", "bow_repel"]
norm = [Vec3(0.0, -1.0, 0.0), Vec3(0.0, 1.0, 0.0), Vec3(-1.0, 0.0, 0.0), Vec3(1.0, 0.0, 0.0), Vec3(0.0, 0.0, -1.0), Vec3(0.0, 0.0, 1.0)]

shear_StrainRate=1e-9#rMean*0.000005
shear_dispRate = shear_StrainRate
v_bottom_Plate = Vec3(-1.0,0.0,0)*shear_dispRate

p0 = 100000 # the iso pressure
normalForce = norm[0]*p0*0.01*0.01

############################ Physical properties ##################################
M_PI = 3.141592653
GM_PoissonsRatio = 0.25;
GM_YoungsModulus = 6.936e5
GM_ShearModulus = GM_YoungsModulus / (2.0*(1.0+GM_PoissonsRatio))
GM_BulkModulus = GM_YoungsModulus / (3.0*(1.0-2*GM_PoissonsRatio))
GM_kpn=GM_YoungsModulus*M_PI
GM_ks=GM_kpn/ (2.0*(1.0+GM_PoissonsRatio))
kn=1e9 #normal stiffness of wall-ball contact

########################### simulation time control #################################
#specify the number of timesteps and the timestep increment:
dt = 0.1*math.sqrt(4/3*math.pi*rmin**3*rhos/(math.pi*GT_YoungsModulus*rmin)) #Sat 17 Oct 2020 02:42:19 PM CST
print 'dt = ', dt
sim.setNumTimeSteps (1000)
sim.setTimeStepSize (dt)
#specify the spatial domain for the simulation:
domain = BoundingBox(Vec3(-0.5,-0.1,-0.04), Vec3(1,0.1,0.12))
sim.setSpatialDomain(bBox=domain, circDimList=[False,False,False])
####################################################
sim.readGeometry("GM.geo") # I wrote the particles and connections in this script

Num = sim.getNumParticles()
print 'total number of particles in the model: ',Num

sim.setParticleDensity(
 tag=1000000,
 mask=-1,
 Density=1000.0*alfa
)

sim.setParticleNonRotational(1000000)

sim.createInteractionGroup(
 RotBondPrms(
  name="gm_bond",
  normalK=GM_kpn,
  shearK=GM_ks,
  torsionK=GM_ks,
  bendingK=GM_kpn,
  normalBrkForce=GM_kpn,
  shearBrkForce=GM_ks,
  torsionBrkForce=GM_ks,
  bendingBrkForce=GM_kpn,
  tag=1,
  scaling=True,
  meanR_scaling=True
  )
)

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

#add translational viscous damping:
sim.createInteractionGroup (
   LinDampingPrms(
      name="damping1",
      viscosity=1.0,
      maxIterations=100
   )
)

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

#create a FieldSaver to store the total kinetic energy of the particles:
sim.createFieldSaver (
 ParticleScalarFieldSaverPrms(
 fieldName="e_kin",
 fileName="01ekin.dat",
 fileFormat="SUM",
 beginTimeStep=0,
 endTimeStep=800000000,
 timeStepIncr=10
 )
)

#add a CheckPointer to store simulation data:
sim.createCheckPointer(
 CheckPointPrms(
  fileNamePrefix = "01snapshot",
  beginTimeStep = 0,
  endTimeStep = 800000000,
  timeStepIncr = 100
 )
)

#execute the simulation:
sim.run()

Question information

Language:
English Edit question
Status:
Solved
For:
ESyS-Particle Edit question
Assignee:
No assignee Edit question
Solved by:
Dion Weatherley
Solved:
2020-10-28
Last query:
2020-10-28
Last reply:
2020-10-23
Dion Weatherley (d-weatherley) said : #1

Hi Yaqiong,

Given that you were able to execute bingle_output.py correctly, ESyS-Particle is installed correctly. The problems you are having are more likely arising from your simulation script and/or your geometry file.

Looking at your script, it is possible that your timestep increment is not small enough. You have set dt like this:
dt = 0.1*math.sqrt(4/3*math.pi*rmin**3*rhos/(math.pi*GT_YoungsModulus*rmin))

(I think GT_YoungsModulus should be changed to GM_YoungsModulus)

However, the density of your particles is 1000.0*alfa, which is larger than rhos (=910.0*alpha). Also, the maximum stiffness in your model is math.pi*GM_YoungsModulus*rmax (not rmin). Consequently, I would set dt like this:
dt = 0.1*math.sqrt(4/3*math.pi*rmin**3*1000.0*alfa/(math.pi*GM_YoungsModulus*rmax))

Non-zero initial kinetic energy also may be expected if the bonded particles in your geometry file are not all separated by their equilibrium distance (r0 = r1 + r2). This can often happen just due to round-off errors induced by defining positions with a low number of decimal places in the geometry file. Generally this is not a major problem, particularly if you are using damping. These initial fluctuations in kinetic energy will be very low amplitude and should decay quickly. You may not have observed this with your previous installation because older versions of ESyS-Particle set the equilibrium distance equal to the initial separation of two bonded particles.

I would also recommend that you convert from using RotBondedPrms to using BrittleBeamPrms. The latter interaction is mathematically identical but takes fewer input parameters that are easier to calibrate:
BrittleBeamPrms (
   name = 'pp_bonds',
   youngsModulus = GM_YoungsModulus,
   poissonsRatio = GM_PoissonsRatio,
   cohesion = GM_cohesiveStrength,
   tanAngle = GM_tanFrictionAngle,
   tag = 1
)
You will need to specify the strength of bonds using parameters GM_cohesiveStrength (in stress units; e.g. 100MPa) and GM_tanFrictionAngle (I would usually set this equal to 1).

There is also a corresponding FrictionPrms, that takes similar parameters:
FrictionPrms (
   name = 'pp_friction',
   youngsModulus = GM_YoungsModulus,
   poissonsRatio = GM_PoissonsRatio,
   dynamicMu = 0.6,
   staticMu = 0.6
)

The scaling of elastic stiffnesses and breaking forces is calculated internally when using these interaction groups, according to linear elastic beam theory and a Mohr-Coulomb failure criterion. Generally these two interactions work very well and have been tested for a very broad range of Young's moduli and cohesive strengths.

If you continue to have problems, please post your new script and your geometry file so I can try out your simulation model myself.

Cheers,

Dion

Wang Yaqiong (wangyaqiong) said : #2

Mr Weatherley:

Thank you so much for your answer.

I reinstall ESyS-2.3.5 this morning, and revised the script as your suggestion. But there is still the same problem I met yesterday. The figure output from paraview showed that particles have displacement in x and z direction, and the bond interaction did not break, but it deformed greatly. Also, non-zero initial kinetic energy increased gradually.

here is my script:

#import the appropriate ESyS-Particle modules:
from esys.lsm import *
import math
from esys.lsm.util import *
from esys.lsm.geometry import *
from directshearcontrol import *

#instantiate a simulation object and
#initialise the neighbour search algorithm:
sim = LsmMpi (numWorkerProcesses =1 , mpiDimList = [1,1,1])
sim.initNeighbourSearch (
 particleType = "RotSphere",
 gridSpacing = 0.002, #>=2.5*Rmax+0.2*Rmin
 verletDist = 0.00003 #>=0.2*Rmin
)

############################# constants parameters ##################################
alfa = 1e6
rhos = 910.0*alfa
dMu=0.37; sMu=dMu

########################### geometry ##############################################
R_GT=0.05e-3
R_GM=0.6e-3
############################ Physical properties for GM ##################################
M_PI = 3.141592653
GM_PoissonsRatio = 0.25;
GM_YoungsModulus = 6.936e5
GM_ShearModulus = GM_YoungsModulus / (2.0*(1.0+GM_PoissonsRatio))
GM_BulkModulus = GM_YoungsModulus / (3.0*(1.0-2*GM_PoissonsRatio))
GM_kpn=GM_YoungsModulus*M_PI
GM_ks=GM_kpn/ (2.0*(1.0+GM_PoissonsRatio))
GM_tanFrictionAngle = 1
GM_cohesiveStrength = GM_ks*1e9
kn=1e9 #normal stiffness of wall-ball contact

############################ Physical properties for GT ##################################
GT_PoissonsRatio = 0.15;
GT_YoungsModulus = 0.8385e9
GT_ShearModulus = GT_YoungsModulus / (2.0*(1.0+GT_PoissonsRatio))
GT_BulkModulus = GT_YoungsModulus / (3.0*(1.0-2*GT_PoissonsRatio))
GT_kpn=GT_YoungsModulus*M_PI
GT_ks=GT_kpn/ (2.0*(1.0+GT_PoissonsRatio))
GT_tanFrictionAngle = 1
GT_cohesiveStrength = GT_ks*1e9
########################### simulation time control #################################
#specify the number of timesteps and the timestep increment:

GT_dt = 0.1*math.sqrt(4/3*math.pi*R_GT**3*rhos/(math.pi*GT_YoungsModulus*R_GT)) #Sat 17 Oct 2020 02:42:19 PM CST
GM_dt = 0.1*math.sqrt(4/3*math.pi*R_GM**3*1000.0*alfa/(math.pi*GM_YoungsModulus*R_GM))
print 'dt = ', GM_dt
sim.setNumTimeSteps (100000)
sim.setTimeStepSize (GM_dt)
#specify the spatial domain for the simulation:
domain = BoundingBox(Vec3(-0.5,-0.1,-0.04), Vec3(1,0.1,0.12))
sim.setSpatialDomain(bBox=domain, circDimList=[False,False,False])
####################################################
sim.readGeometry("GM.geo")
#sim.readGeometry("01NWGT.geo")

Num = sim.getNumParticles()
print 'total number of particles in the model: ',Num

sim.setParticleDensity(
 tag=1000000,
 mask=-1,
 Density=1000.0*alfa
)

sim.setParticleDensity(
 tag=10000,
 mask=-1,
 Density=910.0*alfa
)
sim.setParticleDensity(
 tag=10003,
 mask=-1,
 Density=910.0*alfa
)

sim.setParticleNonRotational(1000000)
sim.setParticleNonRotational(10000)
sim.setParticleNonRotational(10003)

#initialise bond interactions for gm particles:

sim.createInteractionGroup(
 BrittleBeamPrms(
  name="gm_bond",
  youngsModulus=GM_YoungsModulus,
  poissonsRatio=GM_PoissonsRatio,
  cohesion=GM_cohesiveStrength,
  tanAngle=GM_tanFrictionAngle,
  tag=1
  )
)

'''
sim.createInteractionGroup(
 BrittleBeamPrms(
  name="fibre_bond",
  youngsModulus=GT_YoungsModulus,
  poissonsRatio=GT_PoissonsRatio,
  cohesion=GT_cohesiveStrength,
  tanAngle=GT_tanFrictionAngle,
  tag=2
  )
)
sim.createInteractionGroup(
 BrittleBeamPrms(
  name="gt_bond",
  youngsModulus=GT_YoungsModulus,
  poissonsRatio=GT_PoissonsRatio,
  cohesion=GT_cohesiveStrength,
  tanAngle=GT_tanFrictionAngle,
  tag=3
  )
)
'''

#initialise frictional interactions for unbonded particles:

sim.createInteractionGroup (
   FrictionPrms(
      name="friction",
      youngsModulus=3.59e9,
      poissonsRatio=0.25,
      dynamicMu=dMu,
      staticMu=sMu
   )
)

#########################################################
sim.createExclusion(
 interactionName1='gm_bond',
 interactionName2='friction'
)

'''
sim.createExclusion(
 interactionName1="fibre_bond",
 interactionName2='friction'
)

sim.createExclusion(
 interactionName1="gt_bond",
 interactionName2='friction'
)
'''
#########################################################

#add translational viscous damping:
sim.createInteractionGroup (
   LinDampingPrms(
      name="damping1",
      viscosity=1.0,
      maxIterations=100
   )
)

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

#create a FieldSaver to store the total kinetic energy of the particles:
sim.createFieldSaver (
 ParticleScalarFieldSaverPrms(
 fieldName="e_kin",
 fileName="01ekin.dat",
 fileFormat="SUM",
 beginTimeStep=0,
 endTimeStep=800000000,
 timeStepIncr=10
 )
)

#add a CheckPointer to store simulation data:
sim.createCheckPointer(
 CheckPointPrms(
  fileNamePrefix = "01snapshot",
  beginTimeStep = 0,
  endTimeStep = 800000000,
  timeStepIncr = 100
 )
)

#create a FieldSaver to wall forces:
RAW2_NormalForcesaver = InteractionVectorFieldSaverPrms(
 interactionName="friction",
 fieldName="normal_force",
 fileName="out_RAW_WITH_normalForce",
 fileFormat="RAW_WITH_POS_ID",
 beginTimeStep=0,
 endTimeStep=800000000,
 timeStepIncr=10000
)
sim.createFieldSaver(RAW2_NormalForcesaver)
#create a FieldSaver to wall forces:
RAW2_NormalForcesaver = InteractionVectorFieldSaverPrms(
 interactionName="friction",
 fieldName="force",
 fileName="out_RAW_WITH_Force",
 fileFormat="RAW_WITH_POS_ID",
 beginTimeStep=0,
 endTimeStep=800000000,
 timeStepIncr=10000
)
sim.createFieldSaver(RAW2_NormalForcesaver)

#execute the simulation:
sim.run()

################################################here is my geo file: the particles have initial overlaps according to the material's facial property#########################################

LSMGeometry 1.2
BoundingBox -0.5 -0.1 -0.04 1 0.1,0.12
PeriodicBoundaries 0 0 0
Dimension 3D
BeginParticles
Simple
560
0.0 -0.0021 0.0 0.0006 100000 1000000
0.0 -0.0021 0.00066 0.0006 100001 1000000
0.0 -0.0021 0.00132 0.0006 100002 1000000
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0.0 -0.0021 0.00264 0.0006 100004 1000000
0.0 -0.0021 0.0033 0.0006 100005 1000000
0.0 -0.0021 0.00396 0.0006 100006 1000000
0.0 -0.0021 0.00462 0.0006 100007 1000000
0.0 -0.0021 0.00528 0.0006 100008 1000000
0.0 -0.0021 0.00594 0.0006 100009 1000000
0.0 -0.0021 0.0066 0.0006 100010 1000000
0.0 -0.0021 0.00726 0.0006 100011 1000000
0.0 -0.0021 0.00792 0.0006 100012 1000000
0.0 -0.0021 0.00858 0.0006 100013 1000000
0.0 -0.0021 0.00924 0.0006 100014 1000000
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0.00066 -0.0021 0.00264 0.0006 100020 1000000
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0.00198 -0.0021 0.0066 0.0006 100058 1000000
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0.00528 -0.0021 0.00792 0.0006 100140 1000000
0.00528 -0.0021 0.00858 0.0006 100141 1000000
0.00528 -0.0021 0.00924 0.0006 100142 1000000
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0.00594 -0.0021 0.00066 0.0006 100145 1000000
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EndConnect

Dion Weatherley (d-weatherley) said : #3

Hi Yaqiong,

Thanks for providing more information. Unfortunately the initial geometry you are trying to construct is the source of the problems you are observing. I can see that the geometry consists of a rectangular grid of particles with bonds joining the corners and diagonals of each cell. The radii of the particles are very large causing considerable initial overlaps. I can see that this is what you intended, but ESyS-Particle is not designed for such geometrical configurations.

ESyS-Particle expects that adjacent particles will just touch each other when in equilibrium. The equilibrium distance between two bonded particles is equal to the sum of their radii. The initial geometry you have provided is far from this equilibrium configuration. The entire geometry is compressed and the diagonal bonds are also far from their equilibrium lengths. Non-zero initial kinetic energy is expected for such a configuration.

My suggestion would be to remove the diagonal bonds and also reduce the radii of all the particles so they are not overlapping initially. This should eliminate the problems you are observing.

Cheers,

Dion

Wang Yaqiong (wangyaqiong) said : #4

Dear Mr Weatherley:

Thank you for your suggestion.

The idea of overlapping particles to generate material comes from that article (Micro-mechanical analysis of geomembrane-sand interactions using DEM. http://dx.doi.org/10.1016/j.compgeo.2017.08.019 ), which also make use of ESyS.

What was weird was that before my reinstallation, when I ran that script, kinetic energy kept zero.

It might be hard for me to give up the idea of overlapping particles, otherwise there would be holes on that material . I wonder if there is other way to solve it.

I will try more times. Thank you Dion !

Yours

Wang Yaqiong (wangyaqiong) said : #5

In another script, the equilibrium distance between two bonded particles is equal to the sum of their radii, but non-zero initial kinetic energy still exists.

Best Dion Weatherley (d-weatherley) said : #6

Hi Yaqiong,

Thanks for sending the link to the paper. I now have a better idea of what you are trying to simulate. Although I have not had time to study the paper in detail, it would appear that the Authors of that paper have implemented some additional features to simulate the geomembrane, which are not available within the official distribution of ESyS-Particle. I am aware of a number of papers by those Authors. They are very adept ESyS-Particle users and maintain a version of the code with a number of bespoke modifications to suit their research needs. I suggest you contact the Authors and ask them for more information about how they modelled the geomembrane and what modifications they made to ESyS-Particle in order to do that.

Regarding the non-zero initial kinetic energy for your two-particle test, it could be due to round-off error. I would need to see the script you used, as well as know which revision of the esys-particle/trunk you have installed on your system. Did you install revision 1217 from the bzr repository (https://code.launchpad.net/esys-particle/trunk) or did you install the stable release tarball from the homepage?

Cheers,

Dion

Wang Yaqiong (wangyaqiong) said : #7

Hi Mr Weatherley,

Thank you so much for your technical support!

I substitute some source code of ESyS, and now there seems to be alright during my simulation!

Cheers,

Yaqiong

Wang Yaqiong (wangyaqiong) said : #8

Thanks Dion Weatherley, that solved my question.