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[Chen Lifan <question693004@xxxxxxxxxxxxxxxxxxxxx>]

New question #693004 on Yade:
https://answers.launchpad.net/yade/+question/693004

Hello:
I have some problems in  the example uniax.py. 
1. I found the number (by the command 'print len(O.bodies)') in the cell isn't the same as the value appointed by sphereInCell. When I change the shape of the packing (i.e. the values in pack.inHyperboloid), the number of speres in the packing changes as well. I wonder the reason for it.
2. How to prepare a 2D packing using pack.randomDensePack? I tried to give the 'dim'  in it a value as 2, but error occured.
Any kind of help is appreciated. Thanks.

Here is the scripts and error:

scripts:

#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import division

from yade import plot,pack,timing
import time, sys, os, copy
readParamsFromTable(noTableOk=True, # unknownOk=True,
	young=24e9,
	poisson=.2,

	sigmaT=3.5e6,
	frictionAngle=atan(0.8),
	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=3,

	specimenLength=.15,
	sphereRadius=3.5e-3,

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

from yade.params.table import *

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


# make geom; the dimensions are hard-coded here; could be in param table if desired
# z-oriented hyperboloid, length 20cm, diameter 10cm, skirt 8cm
# using spheres 7mm of diameter
concreteId=O.materials.append(CpmMat(young=young,frictionAngle=frictionAngle,poisson=poisson,density=4800,sigmaT=sigmaT,relDuctility=relDuctility,epsCrackOnset=epsCrackOnset,isoPrestress=isoPrestress))

sps=SpherePack()
sp=pack.randomDensePack(pack.inHyperboloid((0,0,-.5*specimenLength),(0,0,.5*specimenLength),.5*specimenLength,.17*specimenLength),dim=2,spheresInCell=2000,radius=sphereRadius,memoizeDb='/tmp/triaxPackCache.sqlite',returnSpherePack=True)
#sp=pack.randomDensePack(pack.inAlignedBox((-.25*specimenLength,-.25*specimenLength,-.5*specimenLength),(.25*specimenLength,.25*specimenLength,.5*specimenLength)),spheresInCell=2000,radius=sphereRadius,memoizeDb='/tmp/triaxPackCache.sqlite',returnSpherePack=True)
sp.toSimulation(material=concreteId)
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),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intRadius,label='ss2sc')],
		[Ip2_CpmMat_CpmMat_CpmPhys()],
		[Law2_ScGeom_CpmPhys_Cpm()],
	),
	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'),
]
#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 not plot.data.has_key('sigma'): 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)
			print 'Strengths fc=%g, ft=%g, |fc/ft|=%g'%(fc,ft,abs(fc/ft))
			title=O.tags['description'] if 'description' in 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()

error:

Welcome to Yade 2018.02b 
TCP python prompt on localhost:9000, auth cookie `uaekcd'
XMLRPC info provider on http://localhost:21000
Running script uniax.py
Traceback (most recent call last):
  File "/usr/bin/yade", line 182, in runScript
    execfile(script,globals())
  File "uniax.py", line 78, in <module>
    sp=pack.randomDensePack(pack.inHyperboloid((0,0,-.5*specimenLength),(0,0,.5*specimenLength),.5*specimenLength,.17*specimenLength),dim=2,spheresInCell=2000,radius=sphereRadius,memoizeDb='/tmp/triaxPackCache.sqlite',returnSpherePack=True)
  File "/usr/lib/x86_64-linux-gnu/yade/py/yade/pack.py", line 491, in randomDensePack
    if max(dim)==float('inf'): raise RuntimeError("Infinite predicate and no dimension of packing requested.")
TypeError: 'int' object is not iterable



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