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[Luis Barbosa <question700611@xxxxxxxxxxxxxxxxxxxxx>]

Question #700611 on Yade changed:
https://answers.launchpad.net/yade/+question/700611

    Status: Answered => Open

Luis Barbosa is still having a problem:
For this I have to provide txt files for the creation of the packs.
Sorry for the external links:

====================================================================================

https://drive.google.com/file/d/16y5Ia4kUUm6oap8QlnSvQf9uCuMzJ7TN/view?usp=sharing

https://drive.google.com/file/d/1_rUoO-6b2j6e3LSRsMlh8C4vKRu8txoN/view?usp=sharing

https://drive.google.com/file/d/1oR9bHoru-
Us6wvHwn7UpkZwt9IX6GRvE/view?usp=sharing

https://drive.google.com/file/d/1cLyeXTjNuavGRxuFv27HyPxvtn-2EW5i/view?usp=sharing


=====================================================================================

from yade import pack
from yade import bodiesHandling
from yade import export
from yade import utils
from yade import ymport
import math

############################################
###   DEFINING VARIABLES AND MATERIALS   ###
############################################

# The following 5 lines will be used later for batch execution
nRead=readParamsFromTable(
    num_spheres=3000,# number of spheres
    compFricDegree = 1, # contact friction during the confining phase
    key='_triax_base_', # put you simulation's name here
    unknownOk=True
)
from yade.params import table

num_spheres=table.num_spheres# number of spheres
key=table.key

targetPorosity = 0.50 #the porosity we want for the packing
compFricDegree = table.compFricDegree # initial contact friction during the confining phase (will be decreased during the REFD compaction process)
finalFricDegree = 30 # contact friction during the deviatoric loading
rate=0 # loading rate (strain rate)
damp=0.8 # damping coefficient
stabilityThreshold=0.01 # we test unbalancedForce against this value in different loops (see below)
young=80e5 # contact stiffness200e4
young2=80e5
youngcoat=50e5
bondstr=1000#2e7
bondstr2=1000
bondstrcoat=10


## create materials for spheres and plates
mat=O.materials.append(JCFpmMat(type=1,young=young,poisson=0.3,frictionAngle=radians(compFricDegree),density=2000,tensileStrength=bondstr,cohesion=bondstr,jointNormalStiffness=0,jointShearStiffness=0,jointCohesion=bondstr,jointFrictionAngle=radians(0),jointDilationAngle=0.0,label='spheres'))
O.materials.append(JCFpmMat(type=1,young=20e7,poisson=0.3,frictionAngle=radians(0),density=2600,tensileStrength=0,cohesion=0,jointNormalStiffness=0,jointShearStiffness=0,jointCohesion=0,jointFrictionAngle=radians(0),jointDilationAngle=0.0,label='walls'))
O.materials.append(JCFpmMat(type=1,young=youngcoat,poisson=0.3,frictionAngle=radians(1),density=1500,tensileStrength=bondstrcoat,cohesion=bondstrcoat,jointNormalStiffness=0,jointShearStiffness=0,jointCohesion=bondstrcoat,jointFrictionAngle=radians(0),jointDilationAngle=0.0,label='spherescoat'))

## create walls around the packing

mn,mx=Vector3(0,0,0),Vector3(0.0015,0.0015,0.0015)
mnbox,mxbox=Vector3(0,0,0),Vector3(0.002,0.00195,0.002)
walls=aabbWalls([mnbox,mxbox],thickness=0,material='walls')
wallIds=O.bodies.append(walls)

O.bodies.append(ymport.textExt("matrix_vtest6.txt", format='x_y_z_r', shift=Vector3(0,0.00025,0), scale=1.0,material='spheres',color=(0,1,1)))
O.bodies.append(ymport.textExt("coat_vtest5e5.txt", format='x_y_z_r', shift=Vector3(0,0,0), scale=1.0,material='spherescoat',color=(0,1,1)))


################Particle substitution by large aggregate######################################################################

bodid=[]
for b in O.bodies:
	if b and isinstance(b.shape,Sphere):
#		print (b.shape.radius)
		if b.state.pos[1]>0.00175:
			bodid.append(b.id)
i=0
for p in bodid:
	O.bodies.erase(bodid[i])
	i=i+1

bodid=[]
a=[]
for b in O.bodies:# in sp:
	if b and isinstance(b.shape,Sphere):
#		print (b.shape.radius)
		if b.shape.radius==0.0002:
			bodid.append(b.id)
			a.append(b.state.pos)

i=0
for p in bodid:
	t=a[i]
	f1=O.bodies.append(ymport.textExt("agg2e4_10e6.txt", format='x_y_z_r', shift=t-Vector3(0,0,0.0002), scale=1.0,material='spheres',color=(0,1,1)))
	O.bodies.erase(bodid[i])
	i=i+1

bodiddd=[]
aaa=[]
for bbb in O.bodies:# in sp:
	if bbb and isinstance(bbb.shape,Sphere):
#		print (b.shape.radius)
		if bbb.shape.radius==0.0005:
			bodiddd.append(bbb.id)
			aaa.append(bbb.state.pos)

iii=0
for ppp in bodiddd:
	ttt=aaa[iii]
	f3=O.bodies.append(ymport.textExt("agg5e5_18e6.txt", format='x_y_z_r', shift=ttt-Vector3(0,0,0.0005), scale=1.0,material='spheres',color=(0,1,1)))
	O.bodies.erase(bodiddd[iii])
	iii=iii+1


##############################################################################################################################



#====================================================================================================================================================================

############################
###   DEFINING ENGINES   ###
############################

triax=TriaxialStressController(
    ## TriaxialStressController will be used to control stress and strain. It controls particles size and plates positions.
    ## this control of boundary conditions was used for instance in http://dx.doi.org/10.1016/j.ijengsci.2008.07.002
    maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
    finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
    thickness = 0,

    stressMask = 7,
    internalCompaction=False, # If true the confining pressure is generated by growing particles
    wall_front_activated=True,
    wall_back_activated=True,
    wall_top_activated=True,
    wall_bottom_activated=True,
    wall_left_activated=True,
    wall_right_activated=True,
    goal1=-100,
    goal2=-100,
    goal3=-100,
)

newton=NewtonIntegrator(damping=damp)

O.engines=[

	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
		[Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=-1,label='Physicspheres')],#,xSectionWeibullShapeParameter=1.5, xSectionWeibullScaleParameter=1
		[Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=False)]
	),
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.5),
	triax,
	newton

]

while 1:
    O.run(500,True)

    unb=unbalancedForce()
    triax.goal1=triax.goal2=triax.goal3=triax.meanStress*1.1
    print ('unbalanced force:',unb,' mean stress: ',triax.meanStress,triax.porosity)
    if triax.porosity<targetPorosity:
        break

print ("###    Compacted state saved      ###")
print(triax.stress(3)[1])


setContactFriction(radians(finalFricDegree))

#=======================================

triax.stressMask = 2
triax.wall_bottom_activated=0
#now goal2 is the target strain rate
triax.goal1=rate
triax.goal3=rate
triax.goal2=triax.stress(3)[1]

from yade import plot
O.run(10,True)

#strain is logarithmic strain or true strain which is ls=(ln1+e) where e=dl/L (strain) 
ei0=-triax.strain[0];ei1=-triax.strain[1];ei2=-triax.strain[2]
si0=-triax.stress(0)[0];si1=-triax.stress(2)[1];si2=-triax.stress(4)[2]

## a function saving variables
def history():
    plot.addData(e11=-triax.strain[0]-ei0, e22=-triax.strain[1]-ei1, e33=-triax.strain[2]-ei2,
            ev=-triax.strain[0]-triax.strain[1]-triax.strain[2],
            s11=-triax.stress(triax.wall_right_id)[0]-si0,
            s22=-triax.stress(triax.wall_top_id)[1]-si1,
            s33=-triax.stress(triax.wall_front_id)[2]-si2,
            e=math.exp(-triax.strain[1]-ei1)-1,
            pc=-unsat.bndCondValue[2],
            sw=unsat.getSaturation(isSideBoundaryIncluded=False),
            z1=O.bodies[3].state.pos[1],
            i=O.iter)

if 1:
  ## include a periodic engine calling that function in the simulation loop
  O.engines=O.engines[0:5]+[PyRunner(iterPeriod=20,command='history()',label='recorder')]+O.engines[5:7]

plot.plots={'pc':('sw',None,'e22')}
plot.plot()

#######################################################
##     Drainage Test      ###
#######################################################
##Instantiate a two-phase engine
unsat=TwoPhaseFlowEngine()
#meanDiameter=(O.bodies[-1].shape.radius + O.bodies[6].shape.radius) / 2.

##set boundary conditions, the drainage is controlled by decreasing W-phase pressure and keeping NW-phase pressure constant
unsat.bndCondIsPressure=[0,0,1,1,0,0]
unsat.bndCondIsWaterReservoir=[0,0,1,0,0,0]
unsat.bndCondValue=[0,0,-1e8,0,0,0]
unsat.isPhaseTrapped=True #the W-phase can be disconnected from its reservoir
unsat.surfaceTension = 0.0728
unsat.initialization()
#start invasion, the data of normalized pc-sw-strain will be written into pcSwStrain.txt

f5=open('SwPcTriax710coated3.txt',"w")

ts=O.dt
pgstep= 40
print (pgstep)
pgmax= 9000

for pg in arange(1.0e-8,pgmax,pgstep):
  unsat.bndCondValue=[0,0,(-1.0)*pg,0,0,0]
  unsat.invasion()
  unsat.computeCapillaryForce()
  unsat.meshUpdateInterval=500
  unsat.defTolerance=-1
  unsat.updateTriangulation=True
  print(unsat.getSaturation(isSideBoundaryIncluded=False),pg,-triax.strain[1])

  for b in O.bodies:
    O.forces.setPermF(b.id, unsat.fluidForce(b.id))

  while 1:
    O.run(100,True)
    unb=unbalancedForce()
    if unb<0.1:
      break
  f5.write(str(pg)+" "+str(unsat.getSaturation(isSideBoundaryIncluded=False))+" "+str(triax.strain[1])+"\n")
f5.close()

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