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[Anqi H <question680414@xxxxxxxxxxxxxxxxxxxxx>]

Question #680414 on Yade changed:
https://answers.launchpad.net/yade/+question/680414

Description changed to:
Hey everyone!

I've been trying to create a cubic rock sample of FCC structure, and
apply a 0.5 MPa confining stress to prepare the sample for other
simulations. I tried following the periodic triaxial testing script but
something is not correct in my setup as I'm getting an error message
"body larger than half of the cell size encountered".  I set up the FCC
structure in the rock sample by specifying the centroid position and
radius of every sphere particle, however I'm not sure if this is the
correct way to create the packing. I have attached the my code below, if
anyone could show me some pointers I would really appreciate it.


from yade import pack, qt, plot

r = 0.45
L = 2*sqrt(2)*r
sigmaIso = -5e5

# rock material 
rockID = O.materials.append(CpmMat(young=15e6,poisson=.4,frictionAngle=radians(atan(0.5)),density=2650,label='spheres'))
#wall material
O.materials.append(FrictMat(young=15e6,poisson=.4,frictionAngle=0,density=0,label='frictionless'))
O.periodic = Trus

sphereArr = []

for m in range(0,46): #y axis
	for j in range(0,30): #z  axis
		for i in range(0,15): #x axis
			if j%2==0:
				sphereArr.append((L*i,m*L/2,j*L/2))
			else:
				sphereArr.append((L*(i+(.5)),m*L/2,j*L/2))


O.bodies.append([sphere(center, r,material='spheres',color = (0.42,0.06,0.51) )for center in sphereArr])

## create walls around the packing
walls=aabbWalls([(0,0,0),(20,30,20)],thickness=1e-10,material='frictionless')
wallIds=O.bodies.append(walls)

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom()],
		[Ip2_FrictMat_FrictMat_FrictPhys()],
		[Law2_ScGeom_FrictPhys_CundallStrack()]	
	),
	PeriTriaxController(label='triax',
	goal=(sigmaIso,sigmaIso,sigmaIso),stressMask=7,
	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='GlobalData()',iterPeriod=500),
]

O.dt=.5*PWaveTimeStep()

def GlobalData():
	print 'porosity '+utils.porosity()
	print 'coord #' +utils.avgNumInteractions()


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()

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