Yade

Error while compiling Potential Blocks

Asked by Debdeep Sarkar on 2019-11-25

Hi,

I am trying out an example with Potential Blocks, but I am getting the following error:

File "cubePBscaled.py", line 34, in <module>
    InsertionSortCollider([PotentialBlock2AABB()],verletDist=0.01),
NameError: name 'PotentialBlock2AABB' is not defined

I have already installed the packages coinor-clp and so on. Also I tried to simply write
ENABLE_POTENTIAL_BLOCKS=ON to start the script, as well as
yade cubePBscaled.py ENABLE_POTENTIAL_BLOCKS=ON

However, neither resolved the issue.
Can anyone help me in understanding the issue? My version of Ubuntu is 18.04 and YADE 2018.02b.

Here's the code I am using:
-------------------------------------------------------------------
##!/usr/local/bin/yade-trunk -x
# -*- encoding=utf-8 -*-
# CWBoon 2015

# Uses the following algorithm:
# CW Boon, GT Houlsby, S Utili (2012). A new algorithm for contact detection between convex polygonal and polyhedral particles in the discrete element method. Computers and Geotechnics 44, 73-82.

#Display is saved to a vtk file in the "vtk folder" and the user is required to load it using ParaView. Control the frequency of printing a vtk file using vtkRecorder.iterPeriod in python

#To use this script:
#Compile with
#ENABLE_POTENTIAL_BLOCKS=ON, and add sudo apt-get install
#coinor-clp,
#coinor-libclp-dev,
#coinor-libclp1,
#coinor-libosi1v5

from yade import pack
import math

import os
import errno
try:
 os.mkdir('./vtk/')
except OSError as exc:
 if exc.errno != errno.EEXIST:
  raise
 pass

O.engines=[
 ForceResetter(),
 InsertionSortCollider([PotentialBlock2AABB()],verletDist=0.01),
 InteractionLoop(
  [Ig2_PB_PB_ScGeom(twoDimension=False, unitWidth2D=1.0)],
  [Ip2_FrictMat_FrictMat_KnKsPBPhys(kn_i=1e8, ks_i=1e7, Knormal=1e8, Kshear=1e7, useFaceProperties=False, calJointLength=False, viscousDamping=0.2)],
  [Law2_SCG_KnKsPBPhys_KnKsPBLaw(label='law',neverErase=False, allowViscousAttraction=True, traceEnergy=False)]
 ),
 #GlobalStiffnessTimeStepper(),
 NewtonIntegrator(damping=0.0,exactAsphericalRot=True,gravity=[0,-9.81,0]),
 PotentialBlockVTKRecorder(fileName='./vtk/cubePBscaled',iterPeriod=10000,twoDimension=False,sampleX=50,sampleY=50,sampleZ=50,maxDimension=0.2,label='vtkRecorder')
]

powderDensity = 2000
distanceToCentre = 0.5
meanSize = 1.0
wallThickness = 0.5*meanSize
O.materials.append(FrictMat(young=-1,poisson=-1,frictionAngle=radians(0.0),density=powderDensity,label='frictionless')) #The normal and shear stifness values are determined in the IPhys functor, thus the young, poisson parameters of the FrictMat are not used.
lengthOfBase = 9.0*meanSize
heightOfBase = 14.0*meanSize
sp=pack.SpherePack()
mn,mx=Vector3(-0.5*(lengthOfBase-wallThickness),0.5*meanSize,-0.5*(lengthOfBase-wallThickness)),Vector3(0.5*(lengthOfBase-wallThickness),7.0*heightOfBase,0.5*(lengthOfBase-wallThickness))
R=sqrt(3.0)*distanceToCentre
sp.makeCloud(mn,mx,R,0,100,False)

r=0.01*meanSize
for s in sp:
 b=Body()
 b.mask=1
 b.aspherical=True
 wire=False
 color=Vector3(random.random(),random.random(),random.random())
 highlight=False
 b.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1],
d=[distanceToCentre-r,distanceToCentre-r,distanceToCentre-r,distanceToCentre-r,distanceToCentre-r,distanceToCentre-r], isBoundary=False, color=color,
wire=wire, highlight=highlight, minAabb=sqrt(3)*Vector3(distanceToCentre,distanceToCentre,distanceToCentre), maxAabb=sqrt(3)*Vector3(distanceToCentre,distanceToCentre,distanceToCentre), AabbMinMax=True, fixedNormal=False, id=len(O.bodies))
 utils._commonBodySetup(b, b.shape.volume, b.shape.inertia, material='frictionless',pos=s[0], fixed=False)
 b.state.pos = s[0] #s[0] stores center
 b.state.ori = Quaternion((random.random(),random.random(),random.random()),random.random()) #s[2]
 O.bodies.append(b)

#Bottom faces of the box
r=0.1*wallThickness
bbb=Body()
bbb.mask=3
wire=False
color=[0,0.5,1]
highlight=False
bbb.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), maxAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), fixedNormal=False)
utils._commonBodySetup(bbb, bbb.shape.volume, bbb.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
bbb.state.pos = [0,0,0]
lidID = O.bodies.append(bbb)

b1=Body()
b1.mask=3
wire=False
color=[0,0.5,1]
highlight=False
b1.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), maxAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), fixedNormal=False)
utils._commonBodySetup(b1, b1.shape.volume, b1.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
b1.state.pos = [lengthOfBase/3.0,0,lengthOfBase/3.0]
O.bodies.append(b1)

b2=Body()
b2.mask=3
wire=False
color=[0,0.5,1]
highlight=False
b2.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), maxAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), fixedNormal=False)
utils._commonBodySetup(b2, b2.shape.volume, b2.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
b2.state.pos = [-lengthOfBase/3.0,0,lengthOfBase/3.0]
O.bodies.append(b2)

b3=Body()
b3.mask=3
wire=False
color=[0,0.5,1]
highlight=False
b3.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), maxAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), fixedNormal=False)
utils._commonBodySetup(b3, b3.shape.volume, b3.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
b3.state.pos = [0,0,lengthOfBase/3.0]
O.bodies.append(b3)

b4=Body()
b4.mask=3
wire=False
color=[0,0.5,1]
highlight=False
b4.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), maxAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), fixedNormal=False)
utils._commonBodySetup(b4, b4.shape.volume, b4.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
b4.state.pos = [lengthOfBase/3.0,0,-lengthOfBase/3.0]
O.bodies.append(b4)

b5=Body()
b5.mask=3
wire=False
color=[0,0.5,1]
highlight=False
b5.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), maxAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), fixedNormal=False)
utils._commonBodySetup(b5, b5.shape.volume, b5.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
b5.state.pos = [0,0,-lengthOfBase/3.0]
O.bodies.append(b5)

b6=Body()
b6.mask=3
wire=False
color=[0,0.5,1]
highlight=False
b6.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), maxAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), fixedNormal=False)
utils._commonBodySetup(b6, b6.shape.volume, b6.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
b6.state.pos = [-lengthOfBase/3.0,0,-lengthOfBase/3.0]
O.bodies.append(b6)

b7=Body()
b7.mask=3
wire=False
color=[0,0.5,1]
highlight=False
b7.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), maxAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), fixedNormal=False)
utils._commonBodySetup(b7, b7.shape.volume, b7.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
b7.state.pos = [-lengthOfBase/3.0,0,0]
O.bodies.append(b7)

b8=Body()
b8.mask=3
wire=False
color=[0,0.5,1]
highlight=False
b8.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), maxAabb=1.05*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0), fixedNormal=False)
utils._commonBodySetup(b8, b8.shape.volume, b8.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
b8.state.pos = [lengthOfBase/3.0,0,0]
O.bodies.append(b8)

# Vertical faces A-B-C-D of the box
bA=Body()
bA.mask=3
wire=False
color=[0,0.5,1]
highlight=False
bA.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*wallThickness-r,0.5*wallThickness-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*lengthOfBase-r,0.5*lengthOfBase-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(0.4*wallThickness,0.5*heightOfBase,0.5*lengthOfBase), maxAabb=1.05*Vector3(0.4*wallThickness,0.5*heightOfBase,0.5*lengthOfBase), fixedNormal=False)
utils._commonBodySetup(bA, bA.shape.volume, bA.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
bA.state.pos = [0.5*lengthOfBase,0.5*heightOfBase,0]
O.bodies.append(bA)

bB=Body()
bB.mask=3
wire=False
color=[0,0.5,1]
highlight=False
bB.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*wallThickness-r,0.5*wallThickness-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*lengthOfBase-r,0.5*lengthOfBase-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(0.4*wallThickness,0.5*heightOfBase,0.5*lengthOfBase), maxAabb=1.05*Vector3(0.4*wallThickness,0.5*heightOfBase,0.5*lengthOfBase), fixedNormal=False)
utils._commonBodySetup(bB, bB.shape.volume, bB.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
bB.state.pos = [-0.5*lengthOfBase,0.5*heightOfBase,0]
O.bodies.append(bB)

bC=Body()
bC.mask=3
wire=True
color=[0,0.5,1]
highlight=False
bC.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*lengthOfBase-r,0.5*lengthOfBase-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*wallThickness-r,0.5*wallThickness-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.4*wallThickness), maxAabb=1.05*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.4*wallThickness), fixedNormal=False)
utils._commonBodySetup(bC, bC.shape.volume, bC.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
bC.state.pos = [0,0.5*heightOfBase,0.5*lengthOfBase]
O.bodies.append(bC)

bD=Body()
bD.mask=3
wire=False
color=[0,0.5,1]
highlight=False
bD.shape=PotentialBlock(k=0.0, r=r, R=0.0, a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*lengthOfBase-r,0.5*lengthOfBase-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*wallThickness-r,0.5*wallThickness-r], id=len(O.bodies), isBoundary=True, color=color, wire=wire, highlight=highlight, AabbMinMax=True, minAabb=1.05*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.4*wallThickness), maxAabb=1.05*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.4*wallThickness), fixedNormal=False)
utils._commonBodySetup(bD, bD.shape.volume, bD.shape.inertia, material='frictionless', pos=[0,0,0], fixed=True)
bD.state.pos = [0,0.5*heightOfBase,-0.5*lengthOfBase]
O.bodies.append(bD)

escapeNo=0
def myAddPlotData():
 global escapeNo
 global wallThickness
 global meanSize
 uf=utils.unbalancedForce()
 if isnan(uf):
  uf = 1.0
 KE = utils.kineticEnergy()

 for b in O.bodies:
  if b.state.pos[1] < -5.0*meanSize and len(b.state.blockedDOFs)==0: #i.e. fixed==False
   escapeNo = escapeNo+1
   O.bodies.erase(b.id)
 if O.iter>25000:
  removeLid()
 plot.addData(timeStep1=O.iter,timeStep2=O.iter,timeStep3=O.iter,timeStep4=O.iter,time=O.time,unbalancedForce=uf,kineticEn=KE,outsideNo=escapeNo)

from yade import plot
plot.plots={'timeStep1':('unbalancedForce'),'timeStep2':('kineticEn'),'time':('outsideNo')}
#plot.plot() #Uncomment to view plots
O.engines=O.engines+[PyRunner(iterPeriod=10,command='myAddPlotData()')]

def removeLid():
 global lidID
 if (O.bodies[lidID]):
  O.bodies.erase(lidID)

O.dt = 0.2*sqrt(0.3*O.bodies[0].state.mass/1.0e8)

from yade import qt
qt.Controller()
v=qt.View()

O.saveTmp()

Question information

Language:
English Edit question
Status:
Solved
For:
Yade Edit question
Assignee:
No assignee Edit question
Solved by:
Robert Caulk
Solved:
2019-11-25
Last query:
2019-11-25
Last reply:
2019-11-25
Robert Caulk (rcaulk) said : #1

If you want to use potential blocks, you need to compile the source code with ENABLE_POTENTIAL_BLOCKS=ON. A first step to using Yade successfully is to distinguish between compiling source code [1] and running a python script [2].

[1]https://yade-dem.org/doc/installation.html#source-code
[2]https://yade-dem.org/doc/tutorial-hands-on.html#python-basics

Debdeep Sarkar (debdeep-sarkar-922) said : #2

Hi Robert,

Thank you for your prompt reply. Since I am new to Yade, I might have some questions which are/might seem stupid. Hoping for your patience in this regard.

I have downloaded the trunk version (git clone https://gitlab.com/yade-dev/trunk.git), I found various folders and sub folders inside (one which contains potential blocks) but I still didnt get how to compile the source code with ENABLE_POTENTIAL_BLOCKS=ON.

I tried to run the code in trunk but I had the same problem. What am I doing wrong here? How to actually enable potential blocks?

Regards,
Debdeep.

Robert Caulk (rcaulk) said : #3

Please tell us which of the steps do not work for you in the source code compilation instructions [1]

[1]https://yade-dem.org/doc/installation.html#source-code

Debdeep Sarkar (debdeep-sarkar-922) said : #4

I am trying to undertake the compilation process as mentioned in [1]. I have finished till the starting of compilation (the step marked with: cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk). But after this, I cannot proceed as how to enable potential blocks and subsequently, to run the code.

[1]https://yade-dem.org/doc/installation.html#source-code

Robert Caulk (rcaulk) said : #5

>But after this, I cannot proceed

Please be specific about why you cannot proceed beyond the cmake step.

Debdeep Sarkar (debdeep-sarkar-922) said : #6

By this, I mean the specific command that I am supposed to enter. As mentioned in [1], the next command shows:
cmake -DOPTION1=VALUE1 -DOPTION2=VALUE2

However, I am not sure I get exactly what to type and proceed. By the way, I am still inside the 'build' directory.

[1]https://yade-dem.org/doc/installation.html#source-code

Best Robert Caulk (rcaulk) said : #7

cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk -DENABLE_POTENTIAL_BLOCKS=ON

Debdeep Sarkar (debdeep-sarkar-922) said : #8

Thanks Robert Caulk, that solved my question.

Debdeep Sarkar (debdeep-sarkar-922) said : #9

Thanks Robert for the solution. However, just out of curiosity, I wanted to know that since I am already running a couple of simulations using Yade (triaxial test, pretty time consuming), should I wait for the simulations to finish before compiling the source, or I can carry it out independently of the already running simulations?

Vasileios Angelidakis (vsangelidakis) said : #10

Hi,
The Potential Blocks are enabled in yadedaily, if you want to have a quick look.

In any case, following Robert's detailed suggestions, it would be good to learn how to compile YADE from source, in case you need to use any other feature which is not enabled by default in the standard, pre-packaged YADE stable release (e.g. YADE 2018.02b.).

In the source-code, the Potential Blocks are enabled by default (no need to use: -DENABLE_POTENTIAL_BLOCKS=ON); I will update the documentation to reflect that soon.

In theory, you can compile the source code in parallel with your simulations, but be advised that compilation will require available CPUs and RAM, so make sure you can bear the computational cost of compiling the code in parallel with running your simulations. If you are not in any hurry, I'd say wait :)

All the best,
Vasileios

Debdeep Sarkar (debdeep-sarkar-922) said : #11

Thank you Vasileios for the detailed explanation! I will wait for the current simulations to finish before proceeding with compiling the source code.