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[Luis Barbosa <question260503@xxxxxxxxxxxxxxxxxxxxx>]

Question #260503 on Yade changed:
https://answers.launchpad.net/yade/+question/260503

Luis Barbosa gave more information on the question:
Sorry Bruno,
I'm using Triax and an imported geometry .stl in the same script:

#!/usr/bin/python
# -*- coding: utf-8 -*-

############################################
### DEFINING VARIABLES AND MATERIALS ###
############################################
# The following 5 lines will be used later for batch execution
nRead=readParamsFromTable(
	num_spheres=10000,# number of spheres
	compFricDegree = 30, # 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 = 0.45 #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=0.02 # loading rate (strain rate)
damp=0.2 # damping coefficient
stabilityThreshold=0.01 # we test unbalancedForce against this value in different loops (see below)
young=5e6 # contact stiffness
mn,mx=Vector3(-0.1,0,-0.1),Vector3(0.1,0.3,0.1) # corners of the initial packing

## create materials for spheres and plates
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))

## create walls around the packing
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)

## use a SpherePack object to generate a random loose particles packing
sp=pack.SpherePack()

clumps=False #turn this true for the same example with clumps
if clumps:
	## approximate mean rad of the futur dense packing for latter use
	volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2])
	mean_rad = pow(0.09*volume/num_spheres,0.3333)
	## define a unique clump type (we could have many, see clumpCloud documentation)
	c1=pack.SpherePack([((-0.2*mean_rad,0,0),0.5*mean_rad),((0.2*mean_rad,0,0),0.5*mean_rad)])
	## generate positions and input them in the simulation
	sp.makeClumpCloud(mn,mx,[c1],periodic=False)
	sp.toSimulation(material='spheres')
	O.bodies.updateClumpProperties()#get more accurate clump masses/volumes/inertia
else:
	sp.makeCloud(mn,mx,-1,0.03333,num_spheres,False, 0.85,seed=1) #"seed" make the "random" generation always the same
#	O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp])
	#or alternatively (higher level function doing exactly the same):
	sp.toSimulation(material='spheres')


############################
### 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,
	## switch stress/strain control using a bitmask. What is a bitmask, huh?!
	## Say x=1 if stess is controlled on x, else x=0. Same for for y and z, which are 1 or 0.
	## Then an integer uniquely defining the combination of all these tests is: mask = x*1 + y*2 + z*4
	## to put it differently, the mask is the integer whose binary representation is xyz, i.e.
	## "100" (1) means "x", "110" (3) means "x and y", "111" (7) means "x and y and z", etc.
	stressMask = 7,
	internalCompaction=True, # If true the confining pressure is generated by growing particles
)

newton=NewtonIntegrator(damping=damp)

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
		[Ip2_FrictMat_FrictMat_FrictPhys()],
		[Law2_ScGeom_FrictPhys_CundallStrack()]
	),
	## We will use the global stiffness of each body to determine an optimal timestep (see https://yade-dem.org/w/images/1/1b/Chareyre&Villard2005_licensed.pdf)
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
	triax,
	TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+table.key),
newton
]

#Display spheres with 2 colors for seeing rotations better
Gl1_Sphere.stripes=0
if nRead==0: yade.qt.Controller(), yade.qt.View()

## UNCOMMENT THE FOLLOWING SECTIONS ONE BY ONE
## DEPENDING ON YOUR EDITOR, IT COULD BE DONE
## BY SELECTING THE CODE BLOCKS BETWEEN THE SUBTITLES
## AND PRESSING CTRL+SHIFT+D
#######################################
### APPLYING CONFINING PRESSURE ###
#######################################
#the value of (isotropic) confining stress defines the target stress to be applied in all three directions
triax.goal1=triax.goal2=triax.goal3=10000
while 1:
	O.run(1000, True)
#the global unbalanced force on dynamic bodies, thus excluding boundaries, which are not at equilibrium
	unb=unbalancedForce()
	print 'unbalanced force:',unb,' mean stress: ',triax.meanStress
	if unb<stabilityThreshold and abs(10000-triax.meanStress)/10000<0.001:
 		break
O.save('confinedState'+key+'.yade.gz')
print "### Isotropic state saved ###"

###################################################
### REACHING A SPECIFIED POROSITY PRECISELY ###
###################################################
## We will reach a prescribed value of porosity with the REFD algorithm
## (see http://dx.doi.org/10.2516/ogst/2012032 and
## http://www.geosyntheticssociety.org/Resources/Archive/GI/src/V9I2/GI-V9-N2-Paper1.pdf)
import sys #this is only for the flush() below
while triax.porosity>targetPorosity:
	# we decrease friction value and apply it to all the bodies and contacts
	compFricDegree = 0.95*compFricDegree
	setContactFriction(radians(compFricDegree))
	print "\r Friction: ",compFricDegree," porosity:",triax.porosity,
	sys.stdout.flush()
	# while we run steps, triax will tend to grow particles as the packing
	# keeps shrinking as a consequence of decreasing friction. Consequently
	# porosity will decrease
	O.run(500,1)

O.save('compactedState'+key+'.yade.gz')
print "### Compacted state saved ###"

##############################
### DEVIATORIC LOADING ###
##############################
##We move to deviatoric loading, let us turn internal compaction off to keep particles sizes constant
triax.internalCompaction=False
## Change contact friction (remember that decreasing it would generate instantaneous instabilities)
setContactFriction(radians(finalFricDegree))

from yade import ymport
mesh = 'coneplanosimulationmeters'
rod = O.bodies.append(ymport.stl('rod-'+mesh+'.stl',wire=False,material='walls'))
O.engines=[
   ForceResetter(),
   InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Box_Aabb()]),
   InteractionLoop(
      # handle sphere+sphere and facet+sphere collisions
	[Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
	[Ip2_FrictMat_FrictMat_FrictPhys()],
	[Law2_ScGeom_FrictPhys_CundallStrack()]
   ),
   NewtonIntegrator(gravity=(0,-9.81,0),damping=0.6),
   TranslationEngine(ids=rod,translationAxis=[0,-1,0],velocity=0.1),
]


But for  YADE 1.12 in Ubuntu 14.04LTS didn't work.

Luis

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