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[ehsan benabbas <question685280@xxxxxxxxxxxxxxxxxxxxx>]

New question #685280 on Yade:
https://answers.launchpad.net/yade/+question/685280

Hi everybody,

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

I coded a simple triaxial problem and want to make a video from its 3d view. But I get the following as the output and no video file. When I click on the "play" button, just and error shows up

***************************
output:

ehsan@ehsan:~/Desktop/mycodes/video$ /home/ehsan/yade/install/bin/yade-2019-08-08.git-775ae74 video.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 `aedusk'
XMLRPC info provider on http://localhost:21000
Running script video.py
<WARNING> SpherePack:242 long int SpherePack::makeCloud(Vector3r, Vector3r, Real, Real, int, bool, Real, const std::vector<double>&, const std::vector<double>&, bool, int, Matrix3r): Exceeded 1000 tries to insert non-overlapping sphere to packing. Only 662 spheres were added, although you requested 2000. Trying again with porosity 0.46. The size distribution is being scaled down
<WARNING> SpherePack:242 long int SpherePack::makeCloud(Vector3r, Vector3r, Real, Real, int, bool, Real, const std::vector<double>&, const std::vector<double>&, bool, int, Matrix3r): Exceeded 1000 tries to insert non-overlapping sphere to packing. Only 746 spheres were added, although you requested 2000. Trying again with porosity 0.514. The size distribution is being scaled down
<WARNING> SpherePack:242 long int SpherePack::makeCloud(Vector3r, Vector3r, Real, Real, int, bool, Real, const std::vector<double>&, const std::vector<double>&, bool, int, Matrix3r): Exceeded 1000 tries to insert non-overlapping sphere to packing. Only 915 spheres were added, although you requested 2000. Trying again with porosity 0.5626. The size distribution is being scaled down
<WARNING> SpherePack:242 long int SpherePack::makeCloud(Vector3r, Vector3r, Real, Real, int, bool, Real, const std::vector<double>&, const std::vector<double>&, bool, int, Matrix3r): Exceeded 1000 tries to insert non-overlapping sphere to packing. Only 1086 spheres were added, although you requested 2000. Trying again with porosity 0.60634. The size distribution is being scaled down
<WARNING> SpherePack:242 long int SpherePack::makeCloud(Vector3r, Vector3r, Real, Real, int, bool, Real, const std::vector<double>&, const std::vector<double>&, bool, int, Matrix3r): Exceeded 1000 tries to insert non-overlapping sphere to packing. Only 1305 spheres were added, although you requested 2000. Trying again with porosity 0.645706. The size distribution is being scaled down
<WARNING> SpherePack:242 long int SpherePack::makeCloud(Vector3r, Vector3r, Real, Real, int, bool, Real, const std::vector<double>&, const std::vector<double>&, bool, int, Matrix3r): Exceeded 1000 tries to insert non-overlapping sphere to packing. Only 1581 spheres were added, although you requested 2000. Trying again with porosity 0.681135. The size distribution is being scaled down
The constructor with a shareWidget is deprecated, use the regular contructor instead.
/home/ehsan/yade/install/lib/x86_64-linux-gnu/yade-2019-08-08.git-775ae74/py/yade/plot.py:444: MatplotlibDeprecationWarning: 
The 'verts' kwarg was deprecated in Matplotlib 3.0 and will be removed in 3.2. Use 'marker' instead.
  scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,s=scatterSize,color=line.get_color(),**scatterMarkerKw)
<FATAL ERROR> ThreadRunner:30 void ThreadRunner::run(): Exception occured: 
InsertionSortCollider.verletDist>0, but unable to locate NewtonIntegrator within O.engines.
<ERROR> yadeWrapper.cpp:655 void pyOmega::wait(): Simulation error encountered.
Traceback (most recent call last):
  File "/home/ehsan/yade/install/bin/yade-2019-08-08.git-775ae74", line 336, in runScript
    execfile(script,globals())
  File "/usr/lib/python3/dist-packages/past/builtins/misc.py", line 82, in execfile
    exec_(code, myglobals, mylocals)
  File "video.py", line 98, in <module>
    O.run(5000,True)
RuntimeError: std::exception
[[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h" in 3D view for help), F10 both, F9 generator, F8 plot. ]]

In [1]: <FATAL ERROR> ThreadRunner:30 void ThreadRunner::run(): Exception occured: 
InsertionSortCollider.verletDist>0, but unable to locate NewtonIntegrator within O.engines.

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

My code is:

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

sp=pack.SpherePack()
mn, mx=Vector3(0,0,0), Vector3(10,10,10)
sp.makeCloud(minCorner=mn,maxCorner=mx,rRelFuzz=0.2,num=2000,porosity=0.4)	


O.materials.append(FrictMat(young=15e6,poisson=0.4,frictionAngle=radians(30),density=2600,label='spheres'))	
O.materials.append(FrictMat(young=15e6,poisson=0.4,frictionAngle=0,density=0,label='frictionless'))	

O.bodies.append([sphere(center,rad,material='spheres') for center, rad in sp])

walls=aabbWalls(thickness=1e-10,material='frictionless')	
wallIds=O.bodies.append(walls)	


triax=TriaxialCompressionEngine(
	wall_bottom_id=wallIds[2],
	wall_top_id=wallIds[3],
	wall_left_id=wallIds[0],
	wall_right_id=wallIds[1],
	wall_back_id=wallIds[4],
	wall_front_id=wallIds[5],
	internalCompaction=False,
	sigmaIsoCompaction=-50e3,
	sigmaLateralConfinement=-50e3,
	max_vel=10,
	strainRate=0.01,
	label="triax",
)


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,
	NewtonIntegrator(damping=0.4)
]

O.engines=O.engines[0:5]+[PyRunner(iterPeriod=20,command='history()',label='recorder')]+O.engines[5:7]
#O.engines=O.engines[0:5]+[PyRunner(command='checkUnbalanced()',realPeriod=2)]+O.engines[5:7]
O.engines=O.engines[0:5]+[VTKRecorder(fileName='3d-vtk-',recorders=['all'],iterPeriod=1000)]+O.engines[5:7]
O.engines=O.engines[0:5]+[qt.SnapshotEngine(fileBase='3d-',iterPeriod=200,label='snapshot')]+O.engines[5:7]
O.engines=O.engines[0:5]+[PyRunner(command='finish()',iterPeriod=20000)]+O.engines[5:7]

O.dt=.5*PWaveTimeStep()

qt.View()

def finish():
	makeVideo(snapshot.snapshots,'3d.mpeg',fps=10,bps=10000)
	O.pause()

#rr=yade.qt.Renderer()
#rr.shape=False
#rr.intrPhys=True

def history():
	plot.addData(unbalanced=unbalancedForce(),i=O.iter,**O.energy,
		e11=-triax.strain[0], e22=-triax.strain[1], e33=-triax.strain[2],
		s11=-triax.stress(0)[0], s22=-triax.stress(2)[1], s33=-triax.stress(4)[2],
		Etot=O.energy.total())


#O.trackEnergy=True


def checkUnbalanced():
	if unbalancedForce()<.05:
		O.pause()
		plot.saveDataTxt('bbb.txt.bz2')

for i in O.interactions:
   id1,id2 = i.id1,i.id2
   fn = i.phys.normalForce
   fs = i.phys.shearForce

#plot.plots={'i':('unbalanced'),'i':('s11','s22','s33'),'i':('e11','e22','e33'),'i':(O.energy.keys,None,'Etot')}
plot.plots={'i':('unbalanced'),'i ':('s11','s22','s33'),' i':('e11','e22','e33'),'e22':('s22')}
plot.labels={'unbalanced':'$F_{UB}$' , 's11':'$\sigma_{11}$' , 's22':'$\sigma_{22}$' , 's33':'$\sigma_{33}$' , 'e11':'$\epsilon_{11}$' , 'e22':'$\epsilon_{22}$' , 'e33':'$\epsilon_{33}$'}
#plot.saveGnuplot()

Gl1_Sphere.stripes=True

plot.plot()

O.saveTmp()

O.run(5000,True)
plot.saveDataTxt('results')


#print 'stress difference:', (triax.stress[2]-triax.stress[1])
#print 'mean stress:',(triax.stress[2]+triax.stress[1]+triax.stress[0])/3
#print 'porosity:', porosity()

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

Thank you very much for your help.

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