Re: [Yade-users] [Question #695935]: Floating point exception (core dumped)
Question #695935 on Yade changed: https://answers.launchpad.net/yade/+question/695935 Status: Open => Solved Yuxuan Wen confirmed that the question is solved: Thank you so much Jan!! Your comment has strengthen my confidence on Yadedaily. I am using Yadedaily in Ubuntu 20.04 and the "Floating point exception (core dumped)" shows up. So it seems that the error is due to the version of Ubuntu instead of Yadedaily. I will install the Ubuntu 18.04 rightaway, and the problem can be solved. Thank you so much for you time and patience! Best Regards, Yuxuan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695929]: spheres pass facet
Question #695929 on Yade changed: https://answers.launchpad.net/yade/+question/695929 Status: Open => Solved Othman Sh confirmed that the question is solved: Thank you Jan!. -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695935]: Floating point exception (core dumped)
Question #695935 on Yade changed: https://answers.launchpad.net/yade/+question/695935 Jan Stránský posted a new comment: On Ubuntu 18.04 using yadedaily (Yade 20210217-4980~0ed545f~bionic1), I did not get "Floating point exception"... Jan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695935]: Floating point exception (core dumped)
Question #695935 on Yade changed: https://answers.launchpad.net/yade/+question/695935 Yuxuan Wen posted a new comment: Hello Jan, The code can be run in Yade 2020.1a, but can not be run correctly in Yadedaily. I wonder if it is possible that you could help me to take a look on Yadedaily. It will not take you much time, for the 1st file is about 1 min, and for the 2nd file is about several seconds. I know this is a troublesome request and will make you inconvenient, I am deeply sorry!! But I really have no clue on how to solve the issue or debugging. If you could help me to take a look or just give me some clues to solve this problem, I will be much appreciated!! Otherwise I have no choice but to install the Ubuntu 18.04 and Yade 2018.02b again... Kind Regards, Yuxuan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695929]: spheres pass facet
Question #695929 on Yade changed: https://answers.launchpad.net/yade/+question/695929 Jan Stránský posted a new comment: > how to change the stiffness of the walls? I am assuming I should assign a different material and elastic modulus for the facets exactly. Because Yade uses harmonic mean, stiffness of walls can be safely "infinite" > but I checked the facetCylinder function [1] and it has no "material" parameter. material is hidden in the **kw, "(unused keyword arguments) passed to utils.facet" [1]. utils.facet [2] then have material cheers Jan [2] https://yade-dem.org/doc/yade.utils.html#yade.utils.facet -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695929]: spheres pass facet
Question #695929 on Yade changed:
https://answers.launchpad.net/yade/+question/695929
Status: Needs information => Open
Othman Sh gave more information on the question:
Hi Jan and Robert,
My experimental test set-up is on cylinder compaction so I really need
to use a cylinder in my simulation. I have defined "Material" and the
code copied below works now.
Robert, how to change the stiffness of the walls? I am assuming I should
assign a different material and elastic modulus for the facets but I
checked the facetCylinder function [1] and it has no "material"
parameter.
Thanks for the help,
Othman
[1] https://yade-dem.org/doc/yade.geom.html#yade.geom.facetCylinder
--
from yade import pack, export, ymport, plot
from pprint import pprint
import numpy as np
import matplotlib.pyplot as plt
import time
tic=time.time()
Material=O.materials.append(FrictMat(young = 1e6, poisson = 0.45,frictionAngle
= 0.349, density=2340))
SG=2.34
##cylinder dimensions
radiuscyl=(500e-6/2)
heightcyl=610e-6
##center of cylinder
cx=0
cy=0
cz=0
##Initial cube dimensions ###
mnx=cx-(radiuscyl*1.1)
mny=cy-(radiuscyl*1.1)
mnz=0
mxx=cx+(radiuscyl*1.1)
mxy=cy+(radiuscyl*1.1)
mxz=heightcyl*1.1
spheres #
sp=pack.SpherePack()
# sizes and distribution are from gradation curve of basalt aggregates
###
sizes=1e-6*np.array([1.58*0.98,1.58,3.63,9.16,15.76,22.94,25]) #Diameters of
portlandite
passing=[0,0.1,0.25,0.5,0.75,0.9,1]
sp.makeCloud((mnx,mny,mnz),(mxx,mxy,mxz),psdSizes=sizes,psdCumm=passing)
cylinder extraction
pred=pack.inCylinder((cx,cy,cz),(cx,cy,heightcyl),radiuscyl)
spFilter=filterSpherePack(pred,sp,Material=Material, returnSpherePack=True)
print (len (spFilter))
spFilter.toSimulation(color=(0.533, 0.803, 0.780))
print ("runtime = ", time.time()-tic)
mass=utils.getSpheresMass()
facets #
facets=geom.facetCylinder((cx,cy,heightcyl/2),radiuscyl,heightcyl,segmentsNumber=150,wallMask=4)
cylinder=O.bodies.append(facets)
yade.qt.View()
##creating disks
d1=geom.facetCylinder((cx,cy,heightcyl),radiuscyl*0.99,0,segmentsNumber=300,wallMask=1)
d2=geom.facetCylinder((cy,cx,cz),radiuscyl*0.99,0,segmentsNumber=300,wallMask=1)
disk1IDs= O.bodies.append(d1)
disk2IDs= O.bodies.append(d2)
for i in disk1IDs:
body= O.bodies[i]
body.state.vel = (0,0,-3.5)
for n in disk2IDs:
body= O.bodies[n]
body.state.vel = (0,0,0)
# compaction #
O.dt=.5*utils.PWaveTimeStep()
O.engines=[
ForceResetter(),
InsertionSortCollider([
Bo1_Sphere_Aabb(),
Bo1_Facet_Aabb()
]),
InteractionLoop(
[
Ig2_Sphere_Sphere_ScGeom(),
Ig2_Facet_Sphere_ScGeom(),
],
[
Ip2_FrictMat_FrictMat_FrictPhys(),
Ip2_FrictMat_FrictMat_FrictPhys(),
],
[
Law2_ScGeom_FrictPhys_CundallStrack(),
],
),
NewtonIntegrator(damping=.3),
# VTKRecorder(fileName='3d-vtk-',recorders=['all'],iterPeriod=500),
PyRunner(iterPeriod=500,command='force()',initRun=True),
]
O.run()
stress=[]
Thickness=[]
Packing_d=[]
def force():
f1= [O.forces.f(i)[2] for i in disk1IDs]
f=np.mean(f1)
s=f/(pi*radiuscyl**2) #stress N/m2
stress.append(s)
thickness=(O.bodies[disk1IDs[1]].state.pos[2])-(O.bodies[disk2IDs[1]].state.pos[2])
packing_density=mass/(thickness*pi*radiuscyl**2)/997/SG
print("stress, thickness, packing density ",s,thickness,packing_density)
Thickness.append(thickness)
Packing_d.append(packing_density)
plot.addData(applied_stress=s,thickness=thickness,packing_density=packing_density)
plot.plots={('applied_stress'):('packing_density')}
plot.plot()
#np.savetxt('compaction_data.txt',np.transpose([stress,Packing_d,Thickness]),delimiter=',')
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Re: [Yade-users] [Question #695935]: Floating point exception (core dumped)
Question #695935 on Yade changed: https://answers.launchpad.net/yade/+question/695935 Jan Stránský posted a new comment: I do not have 20.04, so I am out of testing, sorry.. -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695934]: Compression won't stop when the goal of TriaxialStressController is reached
Question #695934 on Yade changed: https://answers.launchpad.net/yade/+question/695934 Jan Stránský posted a new comment: Yes, the goal seems like (numerical approximation of) rate of the true (logarithmic) strain. For strain rate getting [2] as well as strain rate -> velocity setting [3], current dimensions are used. Anyway, you can easily test it yourself :-) cheers Jan [2] https://gitlab.com/yade-dev/trunk/-/blob/master/pkg/dem/TriaxialStressController.cpp#L39 [3] https://gitlab.com/yade-dev/trunk/-/blob/master/pkg/dem/TriaxialStressController.cpp#L178 -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695827]: CHOLMOD warning: matrix not positive definite with PeriodicFlowEngine
Question #695827 on Yade changed: https://answers.launchpad.net/yade/+question/695827 Katia Boschi gave more information on the question: Dear All, I attach the same script with few particles' sample generation: (Even by running this script with the latest yadedaily package stable version (yade-2021.01a), I get the same error. ) from yade import pack,qt,utils,ymport from yade import export from yade import timing from yade import plot from builtins import range import numpy import time from math import * num_spheres=200 young=750.e6 finalFricDegree = 0.35 graindensity=2600.0 poisson=0.17 en=0.9 sigmaIso=-150.e3 radiusR=0.001/2. D50=radiusR*2.0 O.periodic=True O.cell.setBox(0.01,0.01,0.01) mn,mx=Vector3(0,0,0),Vector3(0.01,0.01,0.01) O.materials.append(FrictViscoMat(young=young,poisson=poisson,frictionAngle=finalFricDegree,density=graindensity,betan=0.0336,label='spheres')) sp=pack.SpherePack() sp.makeCloud(mn, mx, rMean=radiusR, rRelFuzz=0.0, num=num_spheres, periodic=True, seed=1) sp.toSimulation(material='spheres') triax=PeriTriaxController( dynCell=True, mass=0.2, goal=[sigmaIso,sigmaIso,sigmaIso], stressMask=7, globUpdate=5, maxStrainRate=[1,1,1], label='triax') newton=NewtonIntegrator(damping=0.1) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys()], [Law2_ScGeom_FrictViscoPhys_CundallStrackVisco(traceEnergy=True)] ), PeriodicFlowEngine(dead=1,label="flow"), GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.5), triax, newton ] while 1: O.run(1000, True) unb=unbalancedForce() if unb<0.0001: if triax.relStressTol<0.1: break flow.dead=0 flow.pressureForce=True flow.viscousShear=True flow.viscousNormalBodyStress=True flow.viscousShearBodyStress=True flow.normalLubrication=True flow.shearLubrication=True flow.defTolerance=0.1 flow.meshUpdateInterval=200 flow.useSolver=3 flow.permeabilityFactor=1 flow.viscosity=0.0001 flow.bndCondIsPressure=[0,0,0,0,1,1] flow.bndCondValue=[0,0,0,0,0,0] GlobalStiffnessTimeStepper.dead=True O.dt=min(0.5*PWaveTimeStep(),0.5*1./1200.*pi/flow.viscosity*graindensity*(D50/2.)**2) #O.dynDt=True O.run(10,1) while 1: O.run(5000, True) unb=unbalancedForce() if unb<0.0001: if O.cell.velGrad[0,1]<0.01: O.cell.velGrad=O.cell.velGrad+Matrix3(0,0.005,0, 0,0,0, 0,0,0) O.dt=min(0.5*PWaveTimeStep(),0.5*1./1200.*pi/flow.viscosity*graindensity*(D50/2.)**2) if O.cell.velGrad[0,1]>0.01: break -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695935]: Floating point exception (core dumped)
Question #695935 on Yade changed:
https://answers.launchpad.net/yade/+question/695935
Status: Answered => Open
Yuxuan Wen is still having a problem:
Hello Robert and Jan,
Thank you so much for the reply!!! Now I have make a MWE version, I
delete all irrelevant and post-process commands and run the code to make
sure there is no syntax error. I wonder if it is possible that you can
help me to take a look? Thank you so much!
I found that the code can be run in Yade 2020.01a without an error, but
in Yadedaily the "Floating point exception (core dumped)" error shows
up.
The code is shown as follows, there are two files. I run the 1st file
and when it completed I run the 2nd file, since I use the O.save() at
the end of the 1st file and then use the O.load() at the beginning of
the 2nd file. Both the files are in the minimum version. The 1st file
will cost you about 1min (virtual time to 1.67s). And then when you run
the 2nd file by Yadedaily, the "Floating point exception (core dumped)"
error shows up only after a few seconds.
#
first file, 83 lines
---
from yade import pack, plot, qt, export, os
##
lx=0.2
ly=0.2
lz=0.14
target_r=0.005 # target r=0.005m=0.5cm, d=0.01m=1cm, l=20d
target_d=2*target_r
target_phi=0.550
target_e=(1-target_phi)/target_phi
num_spheres=int(lx*ly*lz*target_phi/(4.0/3.0*3.1415926*target_r*target_r*target_r))
## space for generating particle cloud
thickness=target_d # top and bottom walls' thickness
wallsurfh=target_r # distance between wall surface to the cell
mn=Vector3(target_d,target_d,wallsurfh+thickness+target_d)
mx=Vector3(2*lx-target_d,2*ly-target_d,wallsurfh+thickness+2*lz-target_d)
## material properties
density=2650.0 # kg/m3
kn=4e5 # kn/2 is the stiffness of the contact
ks=kn*2.0/7.0
gamma=50.0
cn=4.0/3.0*3.1415926*(0.005*0.005*0.005)*density/4*gamma*2 #0.03469
frict=0
frictnew=26.57 # after stable, change the particle from frictionless to
frictional
## insert periodic cell
O.periodic=True
O.cell.hSize=Matrix3( 2*lx, 0, 0,
0, 2*ly, 0,
0, 0, wallsurfh+thickness+2*lz+thickness+wallsurfh)
## insert the walls for consolidation
O.materials.append(ViscElMat(kn=kn,ks=ks,frictionAngle=radians(frict),cn=cn,cs=0,density=density,label='Box'))
lowbox=O.bodies.append(utils.box(center=(lx,ly,wallsurfh+0.5*thickness),
extents=(5,5,0.5*thickness), fixed=False, material='Box',wire=False))
upbox=O.bodies.append(utils.box(center=(lx,ly,wallsurfh+thickness+2*lz+0.5*thickness),
extents=(5,5,0.5*thickness), fixed=False, material='Box',wire=False))
## use a SpherePack object to generate a random loose particles packing
O.materials.append(ViscElMat(kn=kn,ks=ks,frictionAngle=radians(frict),cn=cn,cs=0,density=density,label='spheres'))
sp=pack.SpherePack()
sp.makeCloud(mn,mx,rMean=target_r,num=num_spheres,periodic=True,seed=1)
O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp])
# define engines #
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()],allowBiggerThanPeriod=True),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
[Ip2_ViscElMat_ViscElMat_ViscElPhys()],
[Law2_ScGeom_ViscElPhys_Basic()]
),
PyRunner(command='servo()',iterPeriod=1),
GlobalStiffnessTimeStepper(),
NewtonIntegrator(damping=0.2),
PyRunner(command='finished()',iterPeriod=200),
]
# define functions #
def servo():
O.bodies[upbox].dynamic=False
O.bodies[lowbox].dynamic=False
if O.cell.size[0] > (lx+1e-8):
rate1=0.5
else:
rate1=0
O.cell.velGrad=Matrix3(-rate1,0,0, 0,-rate1,0, 0,0,0)
if O.bodies[upbox].state.pos[2]-O.bodies[lowbox].state.pos[2]-thickness
> (lz+1e-8):
rate2=0.5
else:
rate2=0
vz=rate2*(O.bodies[upbox].state.pos[2]-O.bodies[lowbox].state.pos[2]-thickness)/2
O.bodies[lowbox].state.vel=(0,0,vz)
O.bodies[upbox].state.vel=(0,0,-vz)
def finished():
if
O.time>=2e4*sqrt(4.0/3.0*3.1415926*target_r*target_r*target_r*density/(kn/2)):
O.save('consolidation.xml')
print ('Consolidation Finished')
O.pause()
#--
2nd file, 67
lines---
from yade import pack, plot, qt, export, os
O.load('consolidation.xml')
step0=O.iter
t0=O.time
rate=0.5
velocity=rate*0.1
radius=O.bodies[2].shape.radius
diameter=2*radius
## delete 2 up and low boxes
Re: [Yade-users] [Question #695934]: Compression won't stop when the goal of TriaxialStressController is reached
Question #695934 on Yade changed: https://answers.launchpad.net/yade/+question/695934 Huang peilun posted a new comment: Thanks Robert, but is the assigned strain rate the rate of the true (logarithmic) strain? -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695935]: Floating point exception (core dumped)
Question #695935 on Yade changed:
https://answers.launchpad.net/yade/+question/695935
Status: Needs information => Answered
Jan Stránský proposed the following answer:
> I was using Ubuntu 18.04 ... my Ubuntu updated to 20.04 automatically
Maybe "accidentally" instead of "automatically? ("automatic upgrade"
does not sound like how Ubuntu (used to?) work)
> If I want to make the code works, should I still install the Yade
2018.02b?
definitely it is an option.
Depending on how you use the Ubuntu (I have there all job and personal data,
program settings, ..., would not want to install it from scratch)
> in Yade 2018.02b ... in Yade 2020.01
you have 2 years of development, some behavior may change. Concerning makeCloud
and seed, there were some bugs / bug fixing [2].
I guess a significant change is Python 2 -> Python 3, which also may break
something in your scripts (e.g. int/float division).
> And then I run the second file. The "Floating point exception (core
dumped)" error will show when running this file:
what is a typical running time of the scripts?
"a lot of files" is not a big problem for mere testing.
Of course, debugging and searching for problem solution is completely different
topic, where a MWE required by Robert would/should help significantly.
Concerning seed in different versions, see the commit [2], the related
bug, date of the commit w.r.t yade versions you use, possibly other
history of this part of the file, ..
cheers
Jan
[2] https://gitlab.com/yade-
dev/trunk/-/commit/cab39356c5b3bec1473b68fdf0b8579d804f03ca
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Re: [Yade-users] [Question #695929]: spheres pass facet
Question #695929 on Yade changed: https://answers.launchpad.net/yade/+question/695929 Jan Stránský posted a new comment: Another option is to use boxes instead of facets - boxes has finite thickness and can help in this situation. Jan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695673]: Contact angle solid liquid phases - 2PFV
Question #695673 on Yade changed: https://answers.launchpad.net/yade/+question/695673 Status: Open => Expired Launchpad Janitor expired the question: This question was expired because it remained in the 'Open' state without activity for the last 15 days. -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695934]: Compression won't stop when the goal of TriaxialStressController is reached
Question #695934 on Yade changed: https://answers.launchpad.net/yade/+question/695934 Status: Open => Answered Robert Caulk proposed the following answer: The TriaxialStressController is functioning according to the docs. You are assigning a strain rate [1]. If you want to stop at a certain strain then you need to use a PyRunner to stop the walls at your desired strain. [1]https://yade- dem.org/doc/yade.wrapper.html#yade.wrapper.TriaxialStressController.stressMask -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695929]: spheres pass facet
Question #695929 on Yade changed: https://answers.launchpad.net/yade/+question/695929 Status: Open => Needs information Robert Caulk requested more information: You also would need a higher stiffness for the walls than the spheres. However, there is no way to know what stiffness you are currently using for your walls since the code you post probably has some kind of python error saying "Material" is not defined. Please send an MWE for more help. -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695935]: Floating point exception (core dumped)
Question #695935 on Yade changed: https://answers.launchpad.net/yade/+question/695935 Status: Open => Needs information Robert Caulk requested more information: Yikes, that's a lot of files. Any chance you can make an MWE [1]? [1]https://www.yade-dem.org/wiki/Howtoask -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
