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Message #08662
Re: [Question #239133]: IndexError
Question #239133 on Yade changed:
https://answers.launchpad.net/yade/+question/239133
Jan Stránský posted a new comment:
Hello,
try to run it also with the tensile part, the IndexError might deend on
this (e.g. the uniax-post.py tried to plot both tension and compression,
saved under 0 and 1 index, but there is only one index present).
cheers
Jan
2013/11/13 pingyang.1019@xxxxxxx <question239133@xxxxxxxxxxxxxxxxxxxxx>
> Question #239133 on Yade changed:
> https://answers.launchpad.net/yade/+question/239133
>
> pingyang.1019@xxxxxxx gave more information on the question:
> Hi
> this is the modified script, can you help me find where the error
> has? I want to run only "uniax-compression" and save
> '/tmp/uniax-compression.yade.gz'
>
>
> from __future__ import division
>
> from yade import utils,plot,pack,timing,eudoxos
> 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
> utils.readParamsFromTable(noTableOk=True, # unknownOk=True,
> young=24e9,
> poisson=.2,
>
> sigmaT=3.5e6,
> frictionAngle=atan(0.8),
> epsCrackOnset=1e-4,
> crackOpening=1e-6,
>
> intRadius=1.5,
> dtSafety=.8,
> damping=0.4,
> strainRateTension=.05,
> strainRateCompression=.5,
> setSpeeds=True,
> # 1=tension, 2=compression (ANDed; 3=both)
> doModes=2,
>
> specimenLength=.1,
> sphereRadius=2e-3,
>
> # isotropic confinement (should be negative)
> isoPrestress=0,
>
> # use the ScGeom variant
> scGeom=False
> )
>
> 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,crackOpening=crackOpening,epsCrackOnset=epsCrackOnset,isoPrestress=isoPrestress))
>
>
> spheres=pack.randomDensePack(pack.inHyperboloid((0,0,-.5*specimenLength),(0,0,.5*specimenLength),.25*specimenLength,.25*specimenLength),spheresInCell=2800,radius=sphereRadius,memoizeDb='/tmp/triaxPackCache.sqlite',material=concreteId)
>
> #spheres=pack.randomDensePack(pack.inAlignedBox((-.25*specimenLength,-.25*specimenLength,-.5*specimenLength),(.25*specimenLength,.25*specimenLength,.5*specimenLength)),spheresInCell=2000,radius=sphereRadius,memoizeDb='/tmp/triaxPackCache.sqlite')
> O.bodies.append(spheres)
> bb=utils.uniaxialTestFeatures()
>
> negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area']
> O.dt=dtSafety*utils.PWaveTimeStep()
> print 'Timestep',O.dt
>
> mm,mx=[pt[axis] for pt in utils.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=utils.approxSectionArea(coord_25,axis),utils.approxSectionArea(coord_50,axis),utils.approxSectionArea(coord_75,axis)
>
> O.engines=[
> ForceResetter(),
>
> InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=intRadius,label='is2aabb'),],verletDist=.05*sphereRadius),
> InteractionLoop(
>
> [Ig2_Sphere_Sphere_Dem3DofGeom(distFactor=intRadius,label='ss2d3dg') if not
> scGeom else
> Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intRadius,label='ss2sc')],
> [Ip2_CpmMat_CpmMat_CpmPhys()],
> [Law2_Dem3DofGeom_CpmPhys_Cpm(epsSoft=0) if not scGeom
> else Law2_ScGeom_CpmPhys_Cpm()],
> ),
> NewtonIntegrator(damping=damping,label='damper'),
> CpmStateUpdater(realPeriod=1),
>
> 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');
>
>
> xmin=-0.025
> xmax=0.025
> ymin=-0.0015
> ymax=0.0015
> zmin=-0.025
> zmax=0.03
> for b in O.bodies:
> if
> ((xmin<b.state.pos[0]<xmax)&(ymin<b.state.pos[1]<ymax)&(zmin<b.state.pos[2]<zmax)):
> print 'Inside sphere ID:', b.id, b.state.pos, '\n'
> O.bodies.erase(b.id)
>
>
> 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
> if not scGeom: ss2d3dg.distFactor=-1.
> else: 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
> # uncomment to get graph for the very first time stopIfDamaged()
> is called
>
> #eudoxos.estimatePoissonYoung(principalAxis=axis,stress=strainer.avgStress,plot=True,cutoff=0.3)
> print O.tags['id'],mode,strainer.strain,sigma[-1]
> 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=='compression' and doModes & 2: # only if
> compression is enabled
> mode='tension'
> O.save('/tmp/uniax-compression.yade.gz')
> print "Saved /tmp/uniax-compression.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)
>
> def addPlotData():
>
> yade.plot.addData({'t':O.time,'i':O.iter,'eps':strainer.strain,'sigma':strainer.avgStress+isoPrestress,
>
> 'sigma.25':utils.forcesOnCoordPlane(coord_25,axis)[axis]/area_25+isoPrestress,
>
> 'sigma.50':utils.forcesOnCoordPlane(coord_50,axis)[axis]/area_50+isoPrestress,
>
> 'sigma.75':utils.forcesOnCoordPlane(coord_75,axis)[axis]/area_75+isoPrestress,
> })
> plot.plot(subPlots=False)
> #O.run()
> initTest()
>
> utils.waitIfBatch()
> At 2013-11-13 15:26:20,"Jan Stránský" <
> question239133@xxxxxxxxxxxxxxxxxxxxx> wrote:
> >Your question #239133 on Yade changed:
> >https://answers.launchpad.net/yade/+question/239133
> >
> > Status: Open => Answered
> >
> >Jan Stránský proposed the following answer:
> >Hello,
> >I have just found, that the script examples/concrete/uniax.py itself is
> not
> >working. Is this also your case?
> >cheers
> >Jan
> >
> >
> >2013/11/13 pingyang.1019@xxxxxxx <question239133@xxxxxxxxxxxxxxxxxxxxx>
> >
> >> New question #239133 on Yade:
> >> https://answers.launchpad.net/yade/+question/239133
> >>
> >> Hi teachers
> >> I run uniax-post.py , but there is a error. I do not know how to
> >> modify .
> >>
> >> Running script /home/py/test/tunnel/uniax-post.py
> >> Traceback (most recent call last):
> >> File "bins/yade-pingyang", line 162, in runScript
> >> execfile(script,globals())
> >> File "/home/py/test/tunnel/uniax-post.py", line 28, in <module>
> >> pylab.figure();
> >> ax,map=post2d.plot(post2d.data(extractDmg,flattener,stDev=2e-3))
> >> File "/home/py/yade/lib/yade-pingyang/py/yade/post2d.py", line 277, in
> >> plot
> >>
> >>
> ct=axes.contour(data['x'],data['y'],data['val'],colors='k',origin='lower',extend='both')
> >> File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 7381, in
> >> contour
> >> return mcontour.QuadContourSet(self, *args, **kwargs)
> >> File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 1112,
> in
> >> __init__
> >> ContourSet.__init__(self, ax, *args, **kwargs)
> >> File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 704,
> in
> >> __init__
> >> self._process_levels()
> >> File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 911,
> in
> >> _process_levels
> >> self._levels.insert(0, min(self.levels[0],self.zmin) - 1)
> >> IndexError: index out of bounds
> >>
> >>
> >> --
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> >> yade-users, which is an answer contact for Yade.
> >>
> >> _______________________________________________
> >> Mailing list: https://launchpad.net/~yade-users
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> >>
> >
> >--
> >If this answers your question, please go to the following page to let us
> >know that it is solved:
> >https://answers.launchpad.net/yade/+question/239133/+confirm?answer_id=0
> >
> >If you still need help, you can reply to this email or go to the
> >following page to enter your feedback:
> >https://answers.launchpad.net/yade/+question/239133
> >
> >You received this question notification because you asked the question.
>
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