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[Robert Caulk <question683687@xxxxxxxxxxxxxxxxxxxxx>]

New question #683687 on Yade:
https://answers.launchpad.net/yade/+question/683687

Hey Yade community,

I am unable to save and reload a FlowEngine based scene. I reproduce the error here using the save-then-reload.py [1] as an example for modifying oedometer.py [2]. 

___The error is as follows:___

>>
GS : j=0 p_moy=-nan dp_moy=-nan
GS iterations : 0
totalForce = 0 0 0
>>

This error suggests that the scene is improperly loaded, considering these GS errors are associated with flow.useSolver=0 [3] (meanwhile the script defines flow.useSolver=3). Further, I've tried re-defining all the flow properties, such as flow.useSolver=3, again after O.load() and before O.run(), but the error does not change. My first thought is that FlowBoundingSphere/Linsolv is not serializable, and therefore we lose all information from the solver class during save/reload. Any ideas?

____The MWE is as follows:____

from __future__ import print_function
from builtins import range
from yade import pack

num_spheres=1000# number of spheres
young=1e6
compFricDegree = 3 # initial contact friction during the confining phase
finalFricDegree = 30 # contact friction during the deviatoric loading
mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing

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'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)

import os.path
savedState = os.path.exists('oedometer_state.yade.gz')

if not savedState:

	sp=pack.SpherePack()
	sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
	sp.toSimulation(material='spheres')

	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()],label="iloop"
		),
		FlowEngine(dead=1,label="flow"),	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
		TriaxialStressController(maxMultiplier=1.+2e4/young, finalMaxMultiplier=1.+2e3/young, thickness = 0,stressMask = 7,max_vel = 0.005,internalCompaction=True,label='triax'),
		NewtonIntegrator(damping=0.2,label='newton')
	]

	triax.goal1=triax.goal2=triax.goal3=-10000

if not savedState:
	while 1:
	  O.run(1000, True)
	  unb=unbalancedForce()
	  if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
	    break

	setContactFriction(radians(finalFricDegree))

	#B. Activate flow engine and set boundary conditions in order to get permeability
	flow.dead=0
	flow.defTolerance=0.3
	flow.meshUpdateInterval=200
	flow.useSolver=3
	flow.permeabilityFactor=1
	flow.viscosity=10
	flow.bndCondIsPressure=[0,0,1,1,0,0]
	flow.bndCondValue=[0,0,1,0,0,0]
	flow.boundaryUseMaxMin=[0,0,0,0,0,0]
	O.dt=0.1e-3
	O.dynDt=False

	O.run(1,1)
	Qin = flow.getBoundaryFlux(2)
	Qout = flow.getBoundaryFlux(3)
	permeability = abs(Qin)/1.e-4 #size is one, we compute K=V/∇H
	print("Qin=",Qin," Qout=",Qout," permeability=",permeability)

	#C. now the oedometer test, drained at the top, impermeable at the bottom plate
	flow.bndCondIsPressure=[0,0,0,1,0,0]
	flow.bndCondValue=[0,0,0,0,0,0]
	flow.updateTriangulation=True #force remeshing to reflect new BC immediately
	newton.damping=0
	
	triax.goal2=-11000
	O.run(1000,1)
	print('saving oedometer state with pore pressure at',flow.getPorePressure((0.5,0.1,0.5)))
	O.save('oedometer_state.yade.gz')
else:
	O.load('oedometer_state.yade.gz')
	print('loaded oedometer state with pore pressure at',flow.getPorePressure((0.5,0.1,0.5)))
	O.run(100,1)


from yade import plot

def history():
	plot.addData(t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000)

O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')]

from yade import plot
plot.plots={'t':('p')}
plot.plot()

[1]https://gitlab.com/yade-dev/trunk/blob/master/examples/simple-scene/save-then-reload.py
[2]https://gitlab.com/yade-dev/trunk/blob/master/examples/FluidCouplingPFV/oedometer.py
[3]https://gitlab.com/yade-dev/trunk/blob/master/lib/triangulation/FlowBoundingSphereLinSolv.ipp#L598


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