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[Zhicheng Gao <question697523@xxxxxxxxxxxxxxxxxxxxx>]

New question #697523 on Yade:
https://answers.launchpad.net/yade/+question/697523

I set a target porosity as a stop criterion and used O.run() to run simulation. In order to avoid the influence of the later Python code, I added O.wait(). However, after adding this command, the graphical interface will be black until it reaches the stop criterion. Is there any way to make the graphical interface display graphics.
Another question, when I run my code, the following warning appears:
/usr/lib/python3/dist-packages/matplotlib/__init__.py:831: MatplotlibDeprecationWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.
  mplDeprecation)
/usr/lib/python3/dist-packages/matplotlib/__init__.py:801: MatplotlibDeprecationWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.
  mplDeprecation)
Why does this happen?
Here is my code:
##______________ First section, generate sample_________

from __future__ import print_function
from yade import pack, qt, plot
from math import *

nRead=readParamsFromTable(
        ## model parameters
        num_spheres=100,
        targetPorosity= .387,
        confiningPressure=-100000,
        ## material parameters
        compFricDegree=15,#contact friction during the confining phase
        finalFricDegree=30,#contact friction during the deviatoric loading
        young=2e8,
        poisson=.2,
        density=2600,
        alphaKr=7.5,
        alphaKtw=0,
	competaRoll=.22,
        finaletaRoll=.22,
        etaTwist=0,
        normalCohesion=0,
        shearCohesion=0,
        ## fluid parameters
        fluidDensity=1000,
        dynamicViscosity=.001,
        ## control parameters
        damp=0,
        stabilityThreshold=.001,
        ## output specifications
        filename='suffusion',
        unknowOk=True
)

from yade.params.table import *

O.periodic=True
O.cell.hSize=Matrix3(.001,0,0, 0,.001,0, 0,0,.001)
# create materials for spheres
#shear strength is the sum of friction and adhesion, so the momentRotationLaw=True
O.materials.append(CohFrictMat(alphaKr=alphaKr,alphaKtw=alphaKtw,density=density,etaRoll=competaRoll,etaTwist=etaTwist,frictionAngle=radians(compFricDegree),momentRotationLaw=True,normalCohesion=normalCohesion,poisson=poisson,shearCohesion=shearCohesion,young=young,label='spheres'))

# generate particles packing
sp=pack.SpherePack()
sp.makeCloud((0,0,0),(.001,.001,.001),psdSizes=[0.00008,0.000125,0.0001592,0.0002003,0.0003153,0.000399,0.000502,0.0005743],psdCumm=[0.0,0.00628,0.0565,0.198,0.721,0.915,0.991,1.0],num=num_spheres,seed=1)
sp.toSimulation(material='spheres')

O.engines=[
        ForceResetter(),
        InsertionSortCollider([Bo1_Sphere_Aabb()]),
        InteractionLoop(
            [Ig2_Sphere_Sphere_ScGeom6D()],
            [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(label='contact',setCohesionNow=False,setCohesionOnNewContacts=False)],
            [Law2_ScGeom6D_CohFrictPhys_CohesionMoment(useIncrementalForm=True,always_use_moment_law=True)],
	),
        PeriodicFlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
        GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
        PeriTriaxController(label='triax',
            # specify target values and whether they are strains or stresses
            goal=(confiningPressure,confiningPressure,confiningPressure), stressMask=7,
            # type of servo-control, the strain rate isn't determined, it shloud check the unbalanced force
            dynCell=True,maxStrainRate=(10,10,10),
            # wait until the unbalanced force goes below this value
            maxUnbalanced=stabilityThreshold,relStressTol=1e-3,
            doneHook='compactionFinished()'
            ),
        NewtonIntegrator(damping=0)
]
qt.View()
# enable energy tracking in the code
O.trackEnergy=True

# define function to record history
def history():
    plot.addData(unbalanced=unbalancedForce(),i=O.iter,exx=-triax.strain[0],
            eyy=-triax.strain[1], ezz=-triax.strain[2],
            sxx=-triax.stress[0],syy=-triax.stress[1],szz=-triax.stress[2],
            ev=-triax.strain[0]-triax.strain[1]-triax.strain[2],
            porosity=porosity(),Etot=O.energy.total(),**O.energy# save all available energy data
            )
O.engines=O.engines+[PyRunner(command='history()', iterPeriod=20)]
# define what to plot
plot.plots={'i':('unbalanced','porosity'),'i ':('sxx','syy','szz'),' i':('exx','eyy','ezz'),' i ':('Etot')}
plot.live=True
plot.setLiveForceAlwaysUpdate(True)
# show the plot
plot.plot()

import sys
def compactionFinished():
    #check the current porosity        
    # if the current porosity is lager than target Porosity and comFricDegree is lager than 10,
    # then we decrease friction value and apply it to all the bodies and contacts,
    # else we decrease rolling friction value.
    global compFricDegree, competaRoll
    if porosity()>targetPorosity and compFricDegree>5:
        # we decrease friction value and apply it to all the bodies and contacts
        compFricDegree=0.95*compFricDegree
        setContactFriction(radians(compFricDegree))
        print('Friction:', compFricDegree,'porosity:', porosity())
        # python syntax, make each step printout
        sys.stdout.flush()
    elif porosity()>targetPorosity:
        # we decrease rolling fiction value and apply it to all the bodies and contacts
        competaRoll=0.95*competaRoll
        for b in O.bodies:
            b.mat.etaRoll=competaRoll
        for i in O.interactions:
            i.phys.etaRoll=competaRoll
        print('Rollingfriction:', b.mat.etaRoll, 'porosity:', porosity())
        sys.stdout.flush()
    else:
	# after sample preparation, save the state
        O.save('compactedState'+filename+'.yade.gz')
        print('Compacted state saved', 'porosity', porosity())
        # next time, called python command
        triax.doneHook=''
        O.pause()
O.run()
O.wait()
plot.saveDataTxt('compactedState'+filename)
##__________________________________second section, deviatoric loading__________________________
# change the contact parameters to the final calibration value
setContactFriction(radians(finalFricDegree))
for b in O.bodies:
    b.mat.etaRoll=finaletaRoll
for i in O.interactions:
    i.phys.etaRoll=finaletaRoll
print(O.cell.hSize,O.cell.trsf)
# set the current cell configuration to be the reference one
O.cell.trsf=Matrix3.Identity
O.run(1,True)
print(O.cell.trsf, triax.strain)
# change control type: keep constant confinement in x,y, 30% compression in z
triax.goal=(confiningPressure,confiningPressure,-.3)
triax.stressMask=3
# allow faster deformation along x,y to better maintain stresses
triax.maxStrainRate=(1.,1.,.01)
# call triaxFinished instead of compactionFinished
triax.doneHook='triaxFinished()'

def triaxFinished():
    O.save('loadedState'+filename+'.yade.gz')
    print('Finished')
    O.pause()


# Reset all plot data; keep plots and labels intact
plot.reset()
O.run(1000,True)
plot.saveDataTxt('loadedState'+filename)

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