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[Huihuang Xia <question625502@xxxxxxxxxxxxxxxxxxxxx>]

Question #625502 on Yade changed:
https://answers.launchpad.net/yade/+question/625502

    Status: Needs information => Open

Huihuang Xia gave more information on the question:
Thanks Robert,

https://answers.launchpad.net/yade/+question/246971, gives a good
example. Thus, I want to do a tri-axial compression on a cubic sample
and filter a stone particle shape using pack.filterSpherePack from this
sample. Is this method correct?

According to
https://github.com/yade/trunk/blob/e4e757f2e98a620e3177b7a36a1d10f69f6a6a28/examples
/triax-tutorial/script-session1.py, here is  a code was used to filter a
sphere from a cubic sample, but this code failed, because it got the
following error:

Desktop/sphere$ yade sphere.py
Welcome to Yade 2016.06a 
TCP python prompt on localhost:9000, auth cookie `ecssdy'
XMLRPC info provider on http://localhost:21000
Running script sphere.py
[[ ^L clears screen, ^U kills line. F12 controller, F11 3d view (use h-key for showing help), F10 both, F9 generator, F8 plot. ]]

Yade [1]: ---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/home/huihuang/YADE/install/lib/x86_64-linux-gnu/yade-2016.06a/py/yade/__init__.pyc in refreshEvent(self)
    190         def zxySlot(self): self.setViewAxes((0,-1,0),(1,0,0))
    191         def refreshEvent(self):
--> 192                 self.refreshValues()
    193                 self.activateControls()
    194         def deactivateControls(self):

/home/huihuang/YADE/install/lib/x86_64-linux-gnu/yade-2016.06a/py/yade/__init__.pyc in refreshValues(self)
    263                         self.iterLabel.setText('#%ld / %ld, %.1f/s %s'%(O.iter,stopAtIter,self.iterPerSec,subStepInfo))
    264                 if t!=float('inf'):
--> 265                         s=int(t); ms=int(t*1000)%1000; us=int(t*1000000)%1000; ns=int(t*1000000000)%1000
    266                         self.virtTimeLabel.setText(u'%03ds%03dm%03dμ%03dn'%(s,ms,us,ns))
    267                 else: self.virtTimeLabel.setText(u'[ ∞ ] ?!')

ValueError: cannot convert float NaN to integer


Here is my code:

from yade import pack
from yade import export

############################################
###   DEFINING VARIABLES AND MATERIALS   ###
############################################

# The following 5 lines will be used later for batch execution
nRead=readParamsFromTable(
	num_spheres=3000,# number of spheres
	compFricDegree = 30, # contact friction during the confining phase
	key='_triax_base_', # put you simulation's name here
	unknownOk=True
)
from yade.params import table

num_spheres=table.num_spheres# number of spheres
key=table.key
targetPorosity = 0.43 #the porosity we want for the packing
compFricDegree = table.compFricDegree # initial contact friction during the confining phase (will be decreased during the REFD compaction process)
finalFricDegree = 30 # contact friction during the deviatoric loading
rate=-0.02 # loading rate (strain rate)
damp=0.2 # damping coefficient
stabilityThreshold=0.01 # we test unbalancedForce against this value in different loops (see below)
young=5e6 # contact stiffness
mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing


## create materials for spheres and plates
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))

## create walls around the packing
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)

## use a SpherePack object to generate a random loose particles packing
global sp
sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp])

############################
###   DEFINING ENGINES   ###
############################

triax=TriaxialStressController(
	## TriaxialStressController will be used to control stress and strain. It controls particles size and plates positions.
	## this control of boundary conditions was used for instance in http://dx.doi.org/10.1016/j.ijengsci.2008.07.002
	maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
	finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
	thickness = 0,
	## switch stress/strain control using a bitmask. What is a bitmask, huh?!
	## Say x=1 if stess is controlled on x, else x=0. Same for for y and z, which are 1 or 0.
	## Then an integer uniquely defining the combination of all these tests is: mask = x*1 + y*2 + z*4
	## to put it differently, the mask is the integer whose binary representation is xyz, i.e.
	## "100" (1) means "x", "110" (3) means "x and y", "111" (7) means "x and y and z", etc.
	stressMask = 7,
	internalCompaction=True, # If true the confining pressure is generated by growing particles
)

newton=NewtonIntegrator(damping=damp)

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
		[Ip2_FrictMat_FrictMat_FrictPhys()],
		[Law2_ScGeom_FrictPhys_CundallStrack()]
	),
	PyRunner(command='stop()',iterPeriod=50),
	## We will use the global stiffness of each body to determine an optimal timestep (see https://yade-dem.org/w/images/1/1b/Chareyre&Villard2005_licensed.pdf)
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
	triax,
	TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+table.key),
	newton
]

#Display spheres with 2 colors for seeing rotations better
Gl1_Sphere.stripes=0
if nRead==0:
	pass

#######################################
###   APPLYING CONFINING PRESSURE   ###
#######################################

#the value of (isotropic) confining stress defines the target stress to be applied in all three directions
triax.goal1=triax.goal2=triax.goal3=-10000

# filter the sphere from sp
pred = pack.inSphere(center=(0.5,0.5,0.5),radius=0.1)
assembly = pack.filterSpherePack(pred,sp,True,mask=100)
assembly.toSimulation()

# export the sphere as a *.txt
def stop():
    if O.iter > 5000:
    	O.pause()
    	export.text('sphere.txt',mask=100)

# 3D view and controller
try:
	qt.Controller()
	qt.View()
except:
	pass

In this code, I only did a simple example filter a sphere from a cubic
sample, because filter a stone particle use the same method.

Thanks in advance,

Huihuang Xia

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