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[Abderrahim AKIL <question702047@xxxxxxxxxxxxxxxxxxxxx>]

Question #702047 on Yade changed:
https://answers.launchpad.net/yade/+question/702047

    Status: Answered => Solved

Abderrahim AKIL confirmed that the question is solved:
Hello, thank you for your answer

###below is the script for the yade simulation

from __future__ import division
from __future__ import print_function

from future import standard_library
standard_library.install_aliases()
from yade import plot,pack,timing
import time, sys, os, copy

#import matplotlib
#matplotlib.rc('text',usetex=True)
#matplotlib.rc('text.latex',preamble=r'\usepackage{concrete}\usepackage{euler}')


# default parameters or from table
readParamsFromTable(noTableOk=True, # unknownOk=True,
	young=7e9,
	poisson=.2,

	sigmaT=1.5e6,
	frictionAngle=atan(0.6),
	epsCrackOnset=1e-4,
	relDuctility=30,

	intRadius=1.5,
	dtSafety=.8,
	damping=0.4,
	strainRateTension=.05,
	strainRateCompression=.5,
	setSpeeds=True,
	# 1=tension, 2=compression (ANDed; 3=both)
	doModes=1,

	specimenLength=50e-3,
	sphereRadius=0.75e-3,

	# isotropic confinement (should be negative)
	isoPrestress=0,
)

from yade.params.table import *

if 'description' in list(O.tags.keys()):
O.tags['id']=O.tags['id']+O.tags['description']

concreteId=O.materials.append(CpmMat(young=young,frictionAngle=frictionAngle,poisson=poisson,density=4800,sigmaT=sigmaT,relDuctility=relDuctility,epsCrackOnset=epsCrackOnset,isoPrestress=isoPrestress))

#create box to fill
mn,mx=Vector3(0,0,0),Vector3(specimenLength,specimenLength,specimenLength) # corners of the initial packing
walls=aabbWalls([mn,mx],thickness=0)
wallIds=O.bodies.append(walls)

#fill it with air-voids
pred=pack.inAlignedBox(mn,mx)
sp=SpherePack()

sp.makeCloud(mn,mx,num=500,rMean=1e-3,rRelFuzz=0.6)

for c,r in sp:
   pred = pred - pack.inSphere(c,r)
# Use the predicate to generate sphere packing inside
sp=SpherePack()
sp=pack.randomDensePack(pred,radius=sphereRadius,spheresInCell=500,memoizeDb='/tmp/triaxPackCache.sqlite',returnSpherePack=True)
sp.toSimulation(material=concreteId,color=(1,1,1))
phiS = getSpheresVolume()
phiS = phiS/(specimenLength)**3
p = porosity()
print(p,phiS)

bb=uniaxialTestFeatures()
negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area']
O.dt=dtSafety*PWaveTimeStep()
print('Timestep',O.dt)

mm,mx=[pt[axis] for pt in aabbExtrema()]
coord_25,coord_50,coord_75=mm+.25*(mx-mm),mm+.5*(mx-mm),mm+.75*(mx-mm)
area_25,area_50,area_75=approxSectionArea(coord_25,axis),approxSectionArea(coord_50,axis),approxSectionArea(coord_75,axis)

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=intRadius,label='is2aabb'),],verletDist=.05*sphereRadius), #Relative enlargement of the bounding box; deactivated if negative.; Functor creating Aabb from Sphere.
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intRadius,label='ss2sc')], #Enlarge both radii by this factor (if >1), to permit creation of distant interactions.InteractionGeometry will be computed when interactionDetectionFactor*(rad1+rad2) > distance, Create/update a ScGeom instance representing the geometry of a contact point between two Spheres s.
		[Ip2_CpmMat_CpmMat_CpmPhys()],
		[Law2_ScGeom_CpmPhys_Cpm()], #Constitutive law for the cpm-model.
	),
	NewtonIntegrator(damping=damping,label='damper'),
	CpmStateUpdater(realPeriod=.5),
	UniaxialStrainer(strainRate=strainRateTension,axis=axis,asymmetry=0,posIds=posIds,negIds=negIds,crossSectionArea=crossSectionArea,blockDisplacements=False,blockRotations=False,setSpeeds=setSpeeds,label='strainer'),
	PyRunner(virtPeriod=1e-6/strainRateTension,realPeriod=1,command='addPlotData()',label='plotDataCollector',initRun=True),
	PyRunner(realPeriod=4,command='stopIfDamaged()',label='damageChecker'),
    #SnapshotEngine(iterPeriod=50,fileBase='/tmp/bulldozer-',label='snapshooter'),
    #VTKRecorder(iterPeriod=100,recorders=['all'],fileName='/tmp/p1-')
]
#O.miscParams=[Gl1_CpmPhys(dmgLabel=False,colorStrain=False,epsNLabel=False,epsT=False,epsTAxes=False,normal=False,contactLine=True)]

# plot stresses in ¼, ½ and ¾ if desired as well; too crowded in the graph that includes confinement, though
plot.plots={'eps':('sigma',)} #,'sigma.50')},'t':('eps')} #'sigma.25','sigma.50','sigma.75')}

O.saveTmp('initial');

O.timingEnabled=False

global mode
mode='tension' if doModes & 1 else 'compression'

def initTest():
	global mode
	print("init")
	if O.iter>0:
		O.wait();
		O.loadTmp('initial')
		print("Reversing plot data"); plot.reverseData()
	else: plot.plot(subPlots=False)
	strainer.strainRate=abs(strainRateTension) if mode=='tension' else -abs(strainRateCompression)
	try:
		from yade import qt
		renderer=qt.Renderer()
		renderer.dispScale=(1000,1000,1000) if mode=='tension' else (100,100,100)
	except ImportError: pass
	print("init done, will now run.")
	O.step(); # to create initial contacts
	# now reset the interaction radius and go ahead
	ss2sc.interactionDetectionFactor=1.
	is2aabb.aabbEnlargeFactor=1.

        O.run()

def stopIfDamaged():
	global mode
	if O.iter<2 or 'sigma' not in plot.data: return # do nothing at the very beginning
	sigma,eps=plot.data['sigma'],plot.data['eps']
	extremum=max(sigma) if (strainer.strainRate>0) else min(sigma)
	minMaxRatio=0.5 if mode=='tension' else 0.5
	if extremum==0: return
	import sys;	sys.stdout.flush()
	if abs(sigma[-1]/extremum)<minMaxRatio or abs(strainer.strain)>(5e-3 if isoPrestress==0 else 5e-2):
		if mode=='tension' and doModes & 2: # only if compression is enabled
			mode='compression'
			O.save('/tmp/uniax-tension.yade.gz')
			print("Saved /tmp/uniax-tension.yade.gz (for use with interaction-histogram.py and uniax-post.py)")
			print("Damaged, switching to compression... "); O.pause()
			# important! initTest must be launched in a separate thread;
			# otherwise O.load would wait for the iteration to finish,
			# but it would wait for initTest to return and deadlock would result
			import _thread; _thread.start_new_thread(initTest,())
			return
		else:
			print("Damaged, stopping.")
			ft,fc=max(sigma),min(sigma)
			if doModes==3:
				print('Strengths fc=%g, ft=%g, |fc/ft|=%g'%(fc,ft,abs(fc/ft)))
			if doModes==2:
				print('Compressive strength fc=%g'%(abs(fc)))
			if doModes==1:
				print('Tensile strength ft=%g'%(abs(ft)))
			title=O.tags['description'] if 'description' in list(O.tags.keys()) else O.tags['params']
			print('gnuplot',plot.saveGnuplot(O.tags['id'],title=title))
			print('Bye.')
			O.pause()
			#sys.exit(0) # results in some threading exception
		
def addPlotData():
	yade.plot.addData({'t':O.time,'i':O.iter,'eps':strainer.strain,'sigma':strainer.avgStress+isoPrestress,
		'sigma.25':forcesOnCoordPlane(coord_25,axis)[axis]/area_25+isoPrestress,
		'sigma.50':forcesOnCoordPlane(coord_50,axis)[axis]/area_50+isoPrestress,
		'sigma.75':forcesOnCoordPlane(coord_75,axis)[axis]/area_75+isoPrestress,
		})
plot.plot(subPlots=False)
#O.run()
initTest()
waitIfBatch()
print('gnuplot',plot.saveGnuplot(O.tags['id']))


##find here the parameters table

description  sphereRadius
r_75 .75e-3
r_80 .80e-3
r_85 .85e-3
r_90 .90e-3

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