Re: [Yade-users] [Question #694506]: Removing particles during thermal cycling

2021-01-18 Thread Zoheir Khademian 
Question #694506 on Yade changed:
https://answers.launchpad.net/yade/+question/694506

Status: Answered => Solved

Zoheir Khademian confirmed that the question is solved:
This solved my problem

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Re: [Yade-users] [Question #694506]: Removing particles during thermal cycling

2020-12-14 Thread Robert Caulk 
Question #694506 on Yade changed:
https://answers.launchpad.net/yade/+question/694506

Status: Open => Answered

Robert Caulk changed the question status:
This should be in an answered state, user must have accidentally clicked
"still need help."

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Re: [Yade-users] [Question #694506]: Removing particles during thermal cycling

2020-12-14 Thread Robert Caulk 
Question #694506 on Yade changed:
https://answers.launchpad.net/yade/+question/694506

Robert Caulk posted a new comment:
>Is it because I did not associate it with the engine? like:
"flow.updateTriangulation=1"?

Yes :-)

>If so, Is "flow.updateTriangulation=1" the same as [1], using
flow.meshUpdateInterval=1 after removing the particle and then return it
to flow.meshUpdateInterval=-1?

flow.updateTriangulation is a boolean, so it is a True or False (but 1
or 0 work too). If it is set to True, the next iteration will force
flowEngine to retriangulate. Then it will set updateTriangulation back
to false.

meshUpdateInterval stays set at the number you choose, and will force
flowEngine to update the triangulation every *meshUpdateInterval*
iterations. This will need to stay at 1 if you are using the full THM
coupling.

Cheers,

Robert

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Re: [Yade-users] [Question #694506]: Removing particles during thermal cycling

2020-12-14 Thread Zoheir Khademian 
Question #694506 on Yade changed:
https://answers.launchpad.net/yade/+question/694506

Status: Answered => Open

Zoheir Khademian is still having a problem:
Robert, thank you so much for the quick reply. I truly appreciate it. I
will recompile it and report back to you after trying the MWE.

> updateTriangulation = 1 Does nothing inside yade. I will let you
brainstorm why that is the case and how to fix it.

Is it because I did not associate it with the engine? like: 
"flow.updateTriangulation=1"?
If so, Is "flow.updateTriangulation=1" the same as [1], using 
flow.meshUpdateInterval=1 after removing the particle and then return it to 
flow.meshUpdateInterval=-1?


[1] 
https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.FlowEngine.meshUpdateInterval

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Re: [Yade-users] [Question #694506]: Removing particles during thermal cycling

2020-12-14 Thread Robert Caulk 
Question #694506 on Yade changed:
https://answers.launchpad.net/yade/+question/694506

Robert Caulk posted a new comment:
Also a side note: your line:

updateTriangulation = 1

Does nothing inside yade. I will let you brainstorm why that is the case
and how to fix it.

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Re: [Yade-users] [Question #694506]: Removing particles during thermal cycling

2020-12-14 Thread Robert Caulk 
Question #694506 on Yade changed:
https://answers.launchpad.net/yade/+question/694506

Status: Open => Answered

Robert Caulk proposed the following answer:
Hey Zoheir,

Thanks for reporting this with a working MWE. I think this is now fixed,
if you want to test before it is merged you can clone and compile the
branch titled "eraseBodyThermalEngine" [1], otherwise you will need to
wait for it to work its way into yadedaily which could take a couple
weeks.

Cheers,

Robert

[1]https://gitlab.com/yade-dev/trunk/-/tree/eraseBodyThermalEngine

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[Yade-users] [Question #694506]: Removing particles during thermal cycling

2020-12-13 Thread Zoheir Khademian 
New question #694506 on Yade:
https://answers.launchpad.net/yade/+question/694506

Hello All,

I would like to remove a particle from an assembly after a few 
Hydro-thermo-mechanical cycles (using thermal and flow engines) and then 
continue cycling the model.  After removing the particle, I enforce 
re-triangulation [1] and then use [2] but I get this error and Yade crushes 
once I continue running the model:

python3.6: /usr/include/boost/smart_ptr/shared_ptr.hpp:734: typename 
boost::detail::sp_member_access::type boost::shared_ptr::operator->() 
const [with T = yade::Body; typename boost::detail::sp_member_access::type = 
yade::Body*]: Assertion `px != 0' failed.
Aborted (core dumped)

I am wondering what I am missing here and would appreciate your help.

Thanks

[1] 
https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.FlowEngineT.updateTriangulation
[2] 
https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.FlowEngine.emulateAction

Here is the MWE:

from yade import pack, ymport, plot, utils, export, timing
import numpy as np

young=5e6
mn,mx=Vector3(0,0,0),Vector3(0.05,0.05,0.05)
O.materials.append(FrictMat(young=young*100,poisson=0.5,frictionAngle=0,density=2600e10,label='walls'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(30),density=2600e10,label='spheres'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()
sp.makeCloud(mn,mx,rMean=0.0015,rRelFuzz=0.333,num=200,seed=11) 
sp.toSimulation(color=(0.752, 0.752, 0.752),material='spheres')

triax=TriaxialStressController(
 maxMultiplier=1.+2e4/young,
 finalMaxMultiplier=1.+2e3/young,
 thickness = 0,
 stressMask = 7,
 internalCompaction=True,
)

O.engines=[
 ForceResetter(),
 
InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1,label='is2aabb'),Bo1_Box_Aabb()]),
 InteractionLoop(
  
[Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1,label='ss2sc'),Ig2_Box_Sphere_ScGeom()],
  [Ip2_FrictMat_FrictMat_FrictPhys()],
  [Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
 ),
 
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.5),
 triax,
 FlowEngine(dead=1,label="flow",multithread=False),
 ThermalEngine(dead=1,label='thermal'),
 NewtonIntegrator(damping=0.5)
]

O.step()
ss2sc.interactionDetectionFactor=-1
is2aabb.aabbEnlargeFactor=-1

tri_pressure = 1000
triax.goal1=triax.goal2=triax.goal3=-tri_pressure
triax.stressMask=7
while 1:
  O.run(1000, True)
  unb=unbalancedForce()
  print('unbalanced force:',unb,' mean stress: ',triax.meanStress)
  if unb<0.1 and abs(-tri_pressure-triax.meanStress)/tri_pressure<0.001:
break

triax.internalCompaction=False

flow.debug=False
# add flow
flow.permeabilityMap = False
flow.pZero = 10
flow.meshUpdateInterval=1
flow.fluidBulkModulus=2.2e9
flow.useSolver=4
flow.permeabilityFactor=-1e-5
flow.viscosity= 0.001
flow.decoupleForces =  False
flow.bndCondIsPressure=[0,0,0,0,1,1]
flow.bndCondValue=[0,0,0,0,10,10]

## Thermal Stuff
flow.bndCondIsTemperature=[0,0,0,0,0,0] 
flow.thermalEngine=True
flow.thermalBndCondValue=[0,0,0,0,0,0] 
flow.tZero=25

flow.dead=0
thermal.dead=1

thermal.conduction=True
thermal.fluidConduction=True
thermal.debug=0
thermal.thermoMech=True
thermal.solidThermoMech = True
thermal.fluidThermoMech = True
thermal.advection=True
thermal.useKernMethod=False
thermal.bndCondIsTemperature=[0,0,0,0,0,1]
thermal.thermalBndCondValue=[0,0,0,0,0,45]
thermal.fluidK = 0.650
thermal.fluidBeta = 2e-5 # 0.0002
thermal.particleT0 = 25
thermal.particleK = 2.0
thermal.particleCp = 710
thermal.particleAlpha = 3.0e-5
thermal.particleDensity = 2700
thermal.tsSafetyFactor = 0 #0.01
thermal.uniformReynolds =10
thermal.minimumThermalCondDist=0


timing.reset()
O.dt=1e-4
O.dynDt=False
thermal.dead=0
flow.emulateAction()

def bodyByPos(x,y,z):
 cBody = O.bodies[1]
 cDist = Vector3(100,100,100)
 for b in O.bodies:
  if isinstance(b.shape, Sphere):
   dist = b.state.pos - Vector3(x,y,z)
   if np.linalg.norm(dist) < np.linalg.norm(cDist):
cDist = dist
cBody = b
 return cBody

bodyOfInterest = bodyByPos(0.025,0.025,0.025)


from yade import plot

def history():
 plot.addData(
  ftemp1=flow.getPoreTemperature((0.025,0.025,0.025)),
  p=flow.getPorePressure((0.025,0.025,0.025)),
  t=O.time,
  i = O.iter,
  bodyOfIntTemp = O.bodies[bodyOfInterest.id].state.temp,
)


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

plot.plots={'t':(('ftemp1','k-'),('bodyOfIntTemp','r-'))} 

plot.plot(subPlots=False)
O.run(5,1)

#Removing one particle
Removedbody = bodyByPos(0.,0.,0.)
O.bodies.erase(Removedbody.id)
updateTriangulation=1
O.run()


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