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[Xu Mengqian <question680191@xxxxxxxxxxxxxxxxxxxxx>]

New question #680191 on Yade:
https://answers.launchpad.net/yade/+question/680191

Hello,all.I plan to consolidate the clumps.But when I put the file in the Yade_2018,it can't consolidation.However,when I put the same file into the Yade_1.11,it can consolidate normally.Could anyone give me some suggestions ?

Here is the file:
from yade import pack,plot,qt,export,ymport
import numpy as np
IsoSigma = -100.
O.periodic=True

# define material
idSand=O.materials.append(FrictMat(young=100e3,poisson=1.,frictionAngle=radians(20),density=2650,label='sand'))

# create particles
sp1=pack.SpherePack()
sp1.makeCloud(maxCorner=(0.0015, 0.0015, 0.0015), psdSizes=[0.00017, 0.000191, 0.0002285, 0.00026, 0.000292, 0.000325, 0.00035], psdCumm=[0.0, 0.1, 0.3, 0.5, 0.6, 0.9, 1], periodic=True,num=5000,seed=1)
sp1.toSimulation(color=(1,0,0),material=idSand)

#### show how to use makeClumpTemplate():

#dyad:
relRadList1 = [1,1]
relPosList1 = [[0.4,0,0],[-0.4,0,0]]

#peanut:
#relRadList2 = [.5,1,.5]
#relPosList2 = [[1,0,0],[0,0,0],[-1,0,0]]

#stick:
#relRadList3 = [1,1,1,1,1]
#relPosList3 = [[0,1,0],[0,2,0],[0,3,0],[0,4,0],[0,5,0]]

templates= []
templates.append(clumpTemplate(relRadii=relRadList1,relPositions=relPosList1))
#templates.append(clumpTemplate(relRadii=relRadList2,relPositions=relPosList2))
#templates.append(clumpTemplate(relRadii=relRadList3,relPositions=relPosList3))

#### show how to use replaceByClumps():
O.bodies.replaceByClumps(templates,[1.],discretization=10)

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom()],
   		[Ip2_FrictMat_FrictMat_FrictPhys()],
   		[Law2_ScGeom_FrictPhys_CundallStrack()]),
#	PyRunner(command='fabric()',iterPeriod=10000),
        GlobalStiffnessTimeStepper(),
	NewtonIntegrator(damping=0.70),
	PeriTriaxController(	goal=(IsoSigma,IsoSigma,IsoSigma), # Vector6 of prescribed final values
				stressMask=3,
				dynCell=True,
				maxStrainRate=(0.3e+0,0.3e+0,0.3e+0),
				maxUnbalanced=0.001,
				relStressTol=1.e-3,
				doneHook='Finished()',
				label='p3d'
	),
#	VTKRecorder(fileName='3d-vtk-',recorders=['all'],iterPeriod=10000),
#	PyRunner(command='strains()',iterPeriod=10000),
#  	PyRunner(command='balls()',iterPeriod=10000),
	PyRunner(command='plotAddData()',iterPeriod=100),
]


def plotAddData():
	plot.addData(
		iter=O.iter,iter_=O.iter,
		sxx=p3d.stress[0],syy=p3d.stress[1],szz=p3d.stress[2],
		exx=O.cell.size[0],eyy=O.cell.size[1],ezz=O.cell.size[2],
		Z=avgNumInteractions(),
		Zm=avgNumInteractions(skipFree=True),
                poros=porosity(),
#      		poros=voxelPorosity(500,(0,0,0),O.cell.size),
		unbalanced=utils.unbalancedForce(),
		t=O.time,
		gWork=O.energy['gravWork'],
		Ep=O.energy['elastPotential'],
		Edamp=O.energy['nonviscDamp'],
		Ediss=O.energy['plastDissip'],
		Ekin=utils.kineticEnergy(),
      		Etot=O.energy.total(),**O.energy
		
	)
	plot.saveDataTxt('macroFile',vars=('t','exx','eyy','ezz','sxx','syy','szz','Z','Zm','poros'))
	plot.saveDataTxt('energyFile',vars=('t','Etot','unbalanced','gWork','Edamp','Ekin'))

O.trackEnergy=True

# plotting 
plot.live=True
plot.plots={'iter':('sxx','syy','szz'),'iter_':('exx','eyy','ezz'), ' iter':('unbalanced'), 
            ' iter ':(O.energy.keys,None,'Etot')
}

def fabric():
	fileNomb='fabric'+str(O.iter)
	f = open(fileNomb,'w')
	f.write('id1 id2 x_cp y_cp z_cp n_x n_y n_z Fn_x Fn_y Fn_z Fs_x Fs_y Fs_z ovp\n')
	for i in O.interactions:
		if not i.isReal: continue
		tacts = i.geom.contactPoint
		nmls = i.geom.normal
		ovp = i.geom.penetrationDepth
		Fn = i.phys.normalForce
		Fs = i.phys.shearForce
		f.write('%-16d %-16d %-16g %-16g %-16g %-16g %-16g %-16g %-16g %-16g %-16g %-16g %-16g %-16g %-16g\n'%(i.id1,
			   i.id2,tacts[0],tacts[1],tacts[2],nmls[0],nmls[1],nmls[2],Fn[0],Fn[1],Fn[2],Fs[0],Fs[1],Fs[2],ovp))
	f.close

def balls():
	fileCalled='ball'+str(O.iter)
	export.text(fileCalled)

def strains():
	fileNome='strain'+str(O.iter)
	f = open(fileNome,'w')
	f.write('b.id velx vely velz rotx roty rotz\n')
	for b in O.bodies:
		if isinstance(b.shape,Sphere):
			vels = b.state.vel
			rots = b.state.rot()
			f.write('%-16d %-16g %-16g %-16g %-16g %-16g %-16g\n'%(b.id, vels[0],vels[1],vels[2],
				   rots[0],rots[1],rots[2]))
	f.close

def Finished():
	O.save('isotropicState.xml')
	print 'Finished'
	print porosity()
	O.pause()
yade.qt.Controller(), yade.qt.View()  
O.run()
plot.plot(subPlots=True)


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