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------------------------------------------------------------
revno: 4029
committer: bchareyre <bruno.chareyre@xxxxxxxxxxxxxxx>
timestamp: Thu 2017-03-30 18:42:26 +0200
message:
  add exemple script for two-phase flow with 2PFV technique, related to Yuan and Chareyre (2017)
added:
  examples/FluidCouplingPFV/drainage-2PFV-Yuan_and_Chareyre_2017.py


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=== added file 'examples/FluidCouplingPFV/drainage-2PFV-Yuan_and_Chareyre_2017.py'
--- examples/FluidCouplingPFV/drainage-2PFV-Yuan_and_Chareyre_2017.py	1970-01-01 00:00:00 +0000
+++ examples/FluidCouplingPFV/drainage-2PFV-Yuan_and_Chareyre_2017.py	2017-03-30 16:42:26 +0000
@@ -0,0 +1,148 @@
+# encoding: utf-8
+# This script demonstrates a simple case of drainage simulation using the "2PFV" two-phase model implemented in UnsaturatedEngine.
+# The script was used to generate the result and supplementary material (video) of [1]. The only difference is the problem size (40k particles in the paper vs. 1k (default) in this version)
+# [1] Yuan, C., & Chareyre, B. (2017). A pore-scale method for hydromechanical coupling in deformable granular media. Computer Methods in Applied Mechanics and Engineering, 318, 1066-1079. (http://www.sciencedirect.com/science/article/pii/S0045782516307216)
+
+import matplotlib; matplotlib.rc('axes',grid=True)
+from yade import pack
+import pylab
+from numpy import *
+
+utils.readParamsFromTable(seed=1,num_spheres=1000,compFricDegree = 15.0)
+from yade.params import table
+
+seed=table.seed
+num_spheres=table.num_spheres# number of spheres
+compFricDegree = table.compFricDegree # initial contact friction during the confining phase (will be decreased during the REFD compaction process)
+confiningS=-1e5
+
+## creat a packing with a specific particle side distribution (PSD)
+psdSizes,psdCumm=[.599,0.6,0.849,0.85,1.0,1.40],[0.,0.35,0.35,0.70,.70,1.]
+sp=pack.SpherePack()
+mn,mx=Vector3(0,0,0),Vector3(10,10,10)
+sp.makeCloud(minCorner=mn,maxCorner=mx,psdSizes=psdSizes,psdCumm=psdCumm,distributeMass=True,num=num_spheres,seed=seed)
+
+## create material #0, which will be used as default
+O.materials.append(FrictMat(young=15e7,poisson=.4,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
+O.materials.append(FrictMat(young=15e7,poisson=.4,frictionAngle=0,density=0,label='frictionless'))
+
+## create walls around the packing
+walls=aabbWalls((mn,mx),thickness=0,material='frictionless')
+wallIds=O.bodies.append(walls)
+
+O.bodies.append([utils.sphere(center,rad,material='spheres') for center,rad in sp])
+
+triax=TriaxialStressController(
+	internalCompaction=True,
+	goal1=confiningS,
+	goal2=confiningS,
+	goal3=confiningS,
+	max_vel=10,
+	label="triax"
+)
+
+newton=NewtonIntegrator(damping=0.4)
+
+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()]
+	),
+	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
+	triax,
+	newton
+]
+
+while 1:
+  O.run(1000,True)
+  unb=unbalancedForce()
+  if unb<0.01 and abs(triax.goal1-triax.meanStress)/abs(triax.goal1)<0.001:
+    break
+
+#############################
+##   REACH NEW EQU. STATE ###
+#############################
+finalFricDegree = 30 # contact friction during the 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))
+
+while 1:
+  O.run(1000,True)
+  unb=unbalancedForce()
+  if unb<0.001 and abs(triax.goal1-triax.meanStress)/abs(triax.goal1)<0.001:
+    break  
+
+triax.depth0=triax.depth
+triax.height0=triax.height
+triax.width0=triax.width
+O.save('1kPacking.yade') #save the packing, which can be reloaded later.
+
+O.run(1000,True)
+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]
+
+from yade import plot
+O.engines=O.engines+[PyRunner(iterPeriod=20,command='history()',dead=1,label='recorder')]
+
+def history():
+  	plot.addData(e11=-triax.strain[0]-ei0, e22=-triax.strain[1]-ei1, e33=-triax.strain[2]-ei2,
+		    s11=-triax.stress(0)[0]-si0,
+		    s22=-triax.stress(2)[1]-si1,
+		    s33=-triax.stress(4)[2]-si2,
+		    pc=-unsat.bndCondValue[2],
+		    sw=unsat.getSaturation(False),
+		    i=O.iter
+		    )
+
+plot.plots={'pc':('sw',None,'e22')}
+plot.plot()
+
+#######################################################
+##     Drainage Test under oedometer conditions     ###
+#######################################################
+##oedometer conditions
+triax.stressMask=2
+triax.goal1=triax.goal3=0
+goalTop=triax.stress(3)[1]
+triax.goal2=goalTop
+triax.wall_bottom_activated=0
+recorder.dead=0
+
+##Instantiate a two-phase engine
+unsat=UnsaturatedEngine()
+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.bndCondValue=[0,0,-1e8,0,0,0]
+unsat.isPhaseTrapped=True #the W-phase can be disconnected from its reservoir
+unsat.initialization()
+unsat.surfaceTension = 10
+
+##start invasion, the data of normalized pc-sw-strain will be written into pcSwStrain.txt
+file=open('pcSwStrain.txt',"w")
+for pg in arange(1.0e-5,15.0,0.1):
+  #increase gaz pressure at the top boundary
+  unsat.bndCondValue=[0,0,(-1.0)*pg*unsat.surfaceTension/meanDiameter,0,0,0]
+  #compute the evolution of interfaces
+  unsat.invasion()
+  #save the phases distribution in vtk format, to be displayed by paraview
+  unsat.savePhaseVtk("./")
+  #compute and apply the capillary forces on each particle
+  unsat.computeCapillaryForce()
+  for b in O.bodies:
+    O.forces.setPermF(b.id, unsat.fluidForce(b.id))
+  #reac
+  while 1:
+    O.run(1000,True)
+    unb=unbalancedForce()
+    if unb<0.01:
+      break
+  file.write(str(pg)+" "+str(unsat.getSaturation(False))+" "+str(triax.strain[1]-ei1)+"\n")
+file.close()