New question #683642 on Yade:
https://answers.launchpad.net/yade/+question/683642

Hello, everyboday!

I am learning a tutorial of Periodic triaxial test 
(https://yade-dem.org/doc/tutorial-examples.html#periodic-triaxial-test).  Here 
is the code:

from __future__ import print_function
sigmaIso=-1e5

#import matplotlib
#matplotlib.use('Agg')

# generate loose packing
from yade import pack, qt, plot

O.periodic=True
sp=pack.SpherePack()
if 0:
        ## uniform distribution
        sp.makeCloud((0,0,0),(2,2,2),rMean=.1,rRelFuzz=.3,periodic=True)
else:
        ## create packing from clumps
        # configuration of one clump
        c1=pack.SpherePack([((0,0,0),.03333),((.03,0,0),.017),((0,.03,0),.017)])
        # make cloud using the configuration c1 (there could c2, c3, ...; 
selection between them would be random)
        sp.makeClumpCloud((0,0,0),(2,2,2),[c1],periodic=True,num=500)

# setup periodic boundary, insert the packing
sp.toSimulation()

O.engines=[
        ForceResetter(),
        InsertionSortCollider([Bo1_Sphere_Aabb()]),
        InteractionLoop(
                [Ig2_Sphere_Sphere_ScGeom()],
                [Ip2_FrictMat_FrictMat_FrictPhys()],
                [Law2_ScGeom_FrictPhys_CundallStrack()]
        ),
        PeriTriaxController(label='triax',
                # specify target values and whether they are strains or stresses
                goal=(sigmaIso,sigmaIso,sigmaIso),stressMask=7,
                # type of servo-control
                dynCell=True,maxStrainRate=(10,10,10),
                # wait until the unbalanced force goes below this value
                maxUnbalanced=.1,relStressTol=1e-3,
                # call this function when goal is reached and the packing is 
stable
                doneHook='compactionFinished()'
        ),
        NewtonIntegrator(damping=.2),
        PyRunner(command='addPlotData()',iterPeriod=100),
]
O.dt=.5*PWaveTimeStep()

def addPlotData():
        plot.addData(unbalanced=unbalancedForce(),i=O.iter,
                sxx=triax.stress[0],syy=triax.stress[1],szz=triax.stress[2],
                exx=triax.strain[0],eyy=triax.strain[1],ezz=triax.strain[2],
                # save all available energy data
                Etot=O.energy.total(),**O.energy
        )

# enable energy tracking in the code
O.trackEnergy=True

# define what to plot
plot.plots={'i':('unbalanced',),'i ':('sxx','syy','szz'),' 
i':('exx','eyy','ezz'),
        # energy plot
        ' i ':(O.energy.keys,None,'Etot'),
}
# show the plot
plot.plot()

def compactionFinished():
        # set the current cell configuration to be the reference one
        O.cell.trsf=Matrix3.Identity
        # change control type: keep constant confinement in x,y, 20% 
compression in z
        triax.goal=(sigmaIso,sigmaIso,-.2)
        triax.stressMask=3
        # allow faster deformation along x,y to better maintain stresses
        triax.maxStrainRate=(1.,1.,.1)
        # next time, call triaxFinished instead of compactionFinished
        triax.doneHook='triaxFinished()'
        # do not wait for stabilization before calling triaxFinished
        triax.maxUnbalanced=10

def triaxFinished():
        print('Finished')
        O.pause()


The triaxial consists of 2 stages, one of the stages is isotropic compaction.  
I want to know whether the porosity is accessed once the compaction is 
finished. If can, how to access the porosity once the compaction is finished in 
triaxial test?  Or whether I can specify the porosity during the compaction?

Thanks!

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