New question #685331 on Yade:
https://answers.launchpad.net/yade/+question/685331

Hello,

I am using Ubuntu 18.04, and Yade 2019-08-08.git-775ae74

I have read the wiki and tutorials, struggle with codes as a beginner in yade 
and asked some questions. Finally, I slightly changed 
https://.../script-session1.py. I got some errors such as syntax ones and fixed 
the, but I get the following error repeatedly as follows now:

ehsan@ehsan:~/Desktop$ /home/ehsan/yade/install/bin/yade-2019-08-08.git-775ae74 
Q.py
Welcome to Yade 2019-08-08.git-775ae74 
Using python version: 3.6.8 (default, Oct  7 2019, 12:59:55) 
[GCC 8.3.0]
TCP python prompt on localhost:9000, auth cookie `yksdca'
XMLRPC info provider on http://localhost:21000
Running script Q.py
The constructor with a shareWidget is deprecated, use the regular contructor 
instead.
Number of elements:  2006
Box Volume:  5.3940427e-317
Box Volume calculated:  1000.0
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
~/yade/install/bin/yade-2019-08-08.git-775ae74 in <module>

NameError: name 'history' is not defined
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
~/yade/install/bin/yade-2019-08-08.git-775ae74 in <module>

NameError: name 'history' is not defined
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
~/yade/install/bin/yade-2019-08-08.git-775ae74 in <module>

NameError: name 'history' is not defined
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
~/yade/install/bin/yade-2019-08-08.git-775ae74 in <module>

.
.
.

Since I have defined "history()", I don't know what is the problem. 
Unfortunately couldn't find the answer by googling it. 
*****************************************************************************
This is my code:

############################################################################################################################
#########               TRIAXIAL PROBLEM, Y IS THE VERTICAL AXIS, X IS THE 
RIGHT AXIS, Z IS THE FRONT AXIS         #########
############################################################################################################################

import numpy as np
import math
from yade import pack, plot, qt, export, utils
from datetime import datetime

######################################################
#########         DEFINING VARIABLES         #########

nRead=readParamsFromTable(
        num_spheres=2000,
        compFricDegree = 30,
        key='_triax_base_',
        unknownOk=True
)

from yade.params import table

num_spheres=table.num_spheres           
key=table.key
targetPorosity = 0.43                   
compFricDegree = table.compFricDegree   
finalFricDegree = 30                    
rate=-0.02                              
damp=0.2                                
stabilityThreshold=0.01                 
young=15e6                      
poisson=0.4
mn,mx=Vector3(0,0,0),Vector3(10,10,10)
sigmaIso=-50e3                          

######################################################
#########         DEFINING MATERIALS         #########

O.materials.append(FrictMat(young=young,poisson=poisson,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
            
O.materials.append(FrictMat(young=young,poisson=poisson,frictionAngle=0,density=0,label='frictionlesswalls'))
                           

####################################################
#########         DEFINING PACKING         #########

walls=aabbWalls([mn,mx],thickness=0,material='frictionlesswalls')               
                
wallIds=O.bodies.append(walls)                                                  
                
sp=pack.SpherePack()
volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2])                              
                
mean_rad = pow(0.09*volume/num_spheres,0.3333)                                  
                                
clumps=False                                                                    
                
if clumps:
    volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2])                          
                
    mean_rad = pow(0.09*volume/num_spheres,0.3333)                              
                        
    
c1=pack.SpherePack([((-0.2*mean_rad,0,0),0.5*mean_rad),((0.2*mean_rad,0,0),0.5*mean_rad)])
  
    sp.makeClumpCloud(mn,mx,[c1],periodic=False)                                
                        
    sp.toSimulation(material='spheres')                                         
                
    O.bodies.updateClumpProperties()                                            
                
else:
    sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1)                
                        
    O.bodies.append([sphere(center,rad,material='spheres') for center,rad in 
sp])

##########################################################
#########         DEFINING TRIAXIAL TEST         #########

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

####################################################
#########         DEFINING ENGINES         #########

newton=NewtonIntegrator(damping=damp)
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,
        TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+table.key),
        newton,
        PyRunner(iterPeriod=20,command='history()',label='recorder'),
        PyRunner(command='checkUnbalanced()',realPeriod=2)
]
Gl1_Sphere.stripes=True                                                         
                        
if nRead==0: yade.qt.Controller(), yade.qt.View()
print ('Number of elements: ', len(O.bodies))
print ('Box Volume: ',  triax.boxVolume)
print ('Box Volume calculated: ', volume)

###############################################################
#########         APPLYING CONFINING PRESSURE         #########

triax.internalCompaction=False                  
setContactFriction=radians(compFricDegree)
triax.stressmask=7
triax.goal1=sigmaIso
triax.goal2=sigmaIso
triax.goal3=sigmaIso
while 1:
    O.run(1000, True)
    unb=unbalancedForce()       
    
meanS=(triax.stress(triax.wall_right_id)[0]+triax.stress(triax.wall_top_id)[1]+triax.stress(triax.wall_front_id)[2])/3
      
    print ('unbalanced force:',unb,' mean stress engine: ',triax.meanStress,' 
mean stress (Calculated): ',meanS)
    print ('porosity=',triax.porosity)
    print ('void ratio=',triax.porosity/(1-triax.porosity))
    print ('-----Phase_01: Isotropic compression 50kPa--(^_^)---')
    if unb<stabilityThreshold and abs(sigmaIso-triax.meanStress)/sigmaIso<0.001:
        break
O.save('confinedPhase'+key+'.xml')
print ('###      Isotropic phase saved      ###')

######################################################
#########         DEVIATORIC LOADING         #########

triax.internalCompaction=False                  
setContactFriction=radians(compFricDegree)      
triax.stressMask = 5                            
triax.goal2=rate                                
triax.goal1=sigmaIso                            
triax.goal3=sigmaIso                    
while 1:
    O.run(1000, True)
    unb=unbalancedForce()       
    axialS=triax.stress(triax.wall_top_id)[1]
    print ('step=', O.iter, 'unbalanced force:',unb,' sigma2: ',axialS, 'q=', 
axialS-sigmaIso)
    print ('axial deformation (%)', (triax.strain[1]-e22Check)*100)
    if abs((triax.strain[1]-e22Check)-0.01)<=0.001:
        O.save('firstpoint.xml')
    if abs((triax.strain[1]-e22Check)-0.02)<=0.001:
        O.save('secondpoint.xml')
    if abs((triax.strain[1]-e22Check)-0.03)<=0.001:
        O.save('thirdpoint.xml')
    if abs((triax.strain[1]-e22Check)-0.05)<=0.001:
        O.save('fourthpoint.xml')
    if triax.strain[1]-e22Check>=0.3 : 
        break
O.save('final.xml')

########################################################
#########         RECORD AND PLOT DATA         #########

qt.View()
def checkUnbalanced():
        if unbalancedForce()<.05:
                O.pause()
                plot.saveDataTxt('bbb.txt.bz2')
def history():                                                                  
                
        plot.addData(e11=-triax.strain[0], e22=-triax.strain[1], 
e33=-triax.strain[2],
                        ev=-triax.strain[0]-triax.strain[1]-triax.strain[2],
                        s11=-triax.stress(triax.wall_right_id)[0],
                        s22=-triax.stress(triax.wall_top_id)[1],
                        s33=-triax.stress(triax.wall_front_id)[2],
                        i=O.iter,unbalanced=unbalancedForce()
)
O.run(5000,True)
plot.plots={'e22':('s11','s22','s33'),'e22':('ev')}                             
                
plot.labels={'s11':'$\sigma_{11}$' , 's22':'$\sigma_{22}$' , 
's33':'$\sigma_{33}$' , 'e11':'$\epsilon_{11}$' , 'e22':'$\epsilon_{22}$' , 
'e33':'$\epsilon_{33}$' , 'ev':'$\epsilon_{V}$'}
plot.plot()                                                                     
                
plot.saveDataTxt('results'+key)                                                 
                
plot.saveGnuplot('plotScript'+key)                                              
                

********************************************************

And also before the error, I get 1 notice as "The constructor with a 
shareWidget is deprecated, use the regular contructor instead.". I don't know 
if this affects my code or not.

Could you please let me know if there is any other mistake in this code?


Thank you very much for your help.

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