How to visualize the deformation in paraview

Hello,

> I generated a VTK files from the uniax.py (concrete/example).

please provide more information (a MWE) [1].

> I would like to ask how can I visualize the deformation in paraview in this case?

For visualization, you need first to export relevant data (particle displacement, microstrain, ...).
It strongly depends on you needs and desire.

Cheers
Jan

[1] https://www.yade-dem.org/wiki/Howtoask

Hello,
Thanks for your response. I would like to ask how can I export this kind of relevant data? I use the following code to export the date:

 VTKRecorder(fileName='3d-vtk-',recorders=['all','cpm'],iterPeriod=100),

what should I add to it to be able to visualize the deformation?

Best regards,
Mahmoud

Everything depends on your definition / requirement of "the deformation" :-)

Two main options, thought:

1) using VTKExporter [2],
- useRef=True (to export particles' original position)
- export particle displacement b.state.displ()
- in Paraview, use WarpByVector to show particle displacement (with possible scale of the value)

2) using [3] (I do not have experience myself)

Cheers
Jan

[2] https://yade-dem.org/doc/yade.export.html#yade.export.VTKExporter.exportSpheres
[3] https://yade-dem.org/doc/user.html#micro-stress-and-micro-strain

I followed [2] to create the VTK output. But when I follow the steps in [2] and I'm facing the problem that I get a black output screen. I can't see the spheres and no VTK files are created. here is the code (the code is uniax code from concrete example and it was working fine before adding the VTKExporter, I added the sign << where you can see where I modify the code):

# -*- encoding=utf-8 -*-
from __future__ import division
from __future__ import print_function

from future import standard_library
standard_library.install_aliases()
from yade import plot,pack,timing
import time, sys, os, copy

#import matplotlib
#matplotlib.rc('text',usetex=True)
#matplotlib.rc('text.latex',preamble=r'\usepackage{concrete}\usepackage{euler}')

"""
A fairly complex script performing uniaxial tension-compression test on hyperboloid-shaped specimen.

Most parameters of the model (and of the setup) can be read from table using yade-multi.

After the simulation setup, tension loading is run and stresses are periodically saved for plotting
as well as checked for getting below the maximum value so far. This indicates failure (see stopIfDamaged
function). After failure in tension, the original setup is loaded anew and the sense of loading reversed.
After failure in compression, strain-stress curves are saved via plot.saveGnuplot and we exit,
giving some useful information like peak stresses in tension/compression.

Running this script for the first time can take long time, as the specimen is prepared using triaxial
compression. Next time, however, an attempt is made to load previously-generated packing
(from /tmp/triaxPackCache.sqlite) and this expensive procedure is avoided.

The specimen length can be specified, its diameter is half of the length and skirt of the hyperboloid is
4/5 of the width.

The particle size is constant and can be specified using the sphereRadius parameter.

The 3d display has displacement scaling applied, so that the fracture looks more spectacular. The scale
is 1000 for tension and 100 for compression.

"""

# default parameters or from table
readParamsFromTable(noTableOk=True, # unknownOk=True,
 young=24e9,
 poisson=.2,

 sigmaT=3.5e6,
 frictionAngle=atan(0.8),
 epsCrackOnset=1e-4,
 relDuctility=30,

 intRadius=1.5,
 dtSafety=.8,
 damping=0.4,
 strainRateTension=.05,
 strainRateCompression=.5,
 setSpeeds=True,
 # 1=tension, 2=compression (ANDed; 3=both)
 doModes=1,

 specimenLength=.15,
 sphereRadius=3.5e-3,

 # isotropic confinement (should be negative)
 isoPrestress=0,
)

from yade.params.table import *

if 'description' in list(O.tags.keys()): O.tags['id']=O.tags['id']+O.tags['description']

concreteId=O.materials.append(CpmMat(young=young,frictionAngle=frictionAngle,poisson=poisson,density=4800,sigmaT=sigmaT,relDuctility=relDuctility,epsCrackOnset=epsCrackOnset,isoPrestress=isoPrestress))

sps=SpherePack()
sp=pack.randomDensePack(pack.inHyperboloid((0,0,-.5*specimenLength),(0,0,.5*specimenLength),.25*specimenLength,.17*specimenLength),spheresInCell=2000,radius=sphereRadius,memoizeDb='/tmp/triaxPackCache.sqlite',returnSpherePack=True)
sp.toSimulation(material=concreteId)
bb=uniaxialTestFeatures()
negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area']
O.dt=dtSafety*PWaveTimeStep()
vtkExporter = export.VTKExporter('baseFileName') <<
print('Timestep',O.dt)

mm,mx=[pt[axis] for pt in aabbExtrema()]
coord_25,coord_50,coord_75=mm+.25*(mx-mm),mm+.5*(mx-mm),mm+.75*(mx-mm)
area_25,area_50,area_75=approxSectionArea(coord_25,axis),approxSectionArea(coord_50,axis),approxSectionArea(coord_75,axis)

O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=intRadius,label='is2aabb'),],verletDist=.05*sphereRadius),
 InteractionLoop(
  [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intRadius,label='ss2sc')],
  [Ip2_CpmMat_CpmMat_CpmPhys()],
  [Law2_ScGeom_CpmPhys_Cpm()],
 ),
 NewtonIntegrator(damping=damping,label='damper'),
 CpmStateUpdater(realPeriod=.5),
 UniaxialStrainer(strainRate=strainRateTension,axis=axis,asymmetry=0,posIds=posIds,negIds=negIds,crossSectionArea=crossSectionArea,blockDisplacements=False,blockRotations=False,setSpeeds=setSpeeds,label='strainer'),
 PyRunner(virtPeriod=1e-6/strainRateTension,realPeriod=1,command='addPlotData()',label='plotDataCollector',initRun=True),
 PyRunner(realPeriod=4,command='stopIfDamaged()',label='damageChecker'),
]
#O.miscParams=[Gl1_CpmPhys(dmgLabel=False,colorStrain=False,epsNLabel=False,epsT=False,epsTAxes=False,normal=False,contactLine=True)]

# plot stresses in ¼, ½ and ¾ if desired as well; too crowded in the graph that includes confinement, though
plot.plots={'eps':('sigma',)} #,'sigma.50')},'t':('eps')} #'sigma.25','sigma.50','sigma.75')}

O.saveTmp('initial');

O.timingEnabled=False

global mode
mode='tension' if doModes & 1 else 'compression'

def initTest():
 global mode
 print("init")
 if O.iter>0:
  O.wait();
  O.loadTmp('initial')
  print("Reversing plot data"); plot.reverseData()
 else: plot.plot(subPlots=False)
 strainer.strainRate=abs(strainRateTension) if mode=='tension' else -abs(strainRateCompression)
 try:
  from yade import qt
  renderer=qt.Renderer()
  renderer.dispScale=(1000,1000,1000) if mode=='tension' else (100,100,100)
 except ImportError: pass
 print("init done, will now run.")
 O.step(); # to create initial contacts
 # now reset the interaction radius and go ahead
 ss2sc.interactionDetectionFactor=1.
 is2aabb.aabbEnlargeFactor=1.

 O.run()

def stopIfDamaged():
 global mode
 if O.iter<2 or 'sigma' not in plot.data: return # do nothing at the very beginning
 sigma,eps=plot.data['sigma'],plot.data['eps']
 extremum=max(sigma) if (strainer.strainRate>0) else min(sigma)
 minMaxRatio=0.5 if mode=='tension' else 0.5
 if extremum==0: return
 import sys; sys.stdout.flush()
 if abs(sigma[-1]/extremum)<minMaxRatio or abs(strainer.strain)>(5e-3 if isoPrestress==0 else 5e-2):
  if mode=='tension' and doModes & 2: # only if compression is enabled
   mode='compression'
   O.save('/tmp/uniax-tension.yade.gz')
   print("Saved /tmp/uniax-tension.yade.gz (for use with interaction-histogram.py and uniax-post.py)")
   print("Damaged, switching to compression... "); O.pause()
   # important! initTest must be launched in a separate thread;
   # otherwise O.load would wait for the iteration to finish,
   # but it would wait for initTest to return and deadlock would result
   import _thread; _thread.start_new_thread(initTest,())
   return
  else:
   print("Damaged, stopping.")
   ft,fc=max(sigma),min(sigma)
   if doModes==3:
    print('Strengths fc=%g, ft=%g, |fc/ft|=%g'%(fc,ft,abs(fc/ft)))
   if doModes==2:
    print('Compressive strength fc=%g'%(abs(fc)))
   if doModes==1:
    print('Tensile strength ft=%g'%(abs(ft)))
   title=O.tags['description'] if 'description' in list(O.tags.keys()) else O.tags['params']
   print('gnuplot',plot.saveGnuplot(O.tags['id'],title=title))
   print('Bye.')
   O.pause()
   #sys.exit(0) # results in some threading exception

def addPlotData():
 yade.plot.addData({'t':O.time,'i':O.iter,'eps':strainer.strain,'sigma':strainer.avgStress+isoPrestress,
  'sigma.25':forcesOnCoordPlane(coord_25,axis)[axis]/area_25+isoPrestress,
  'sigma.50':forcesOnCoordPlane(coord_50,axis)[axis]/area_50+isoPrestress,
  'sigma.75':forcesOnCoordPlane(coord_75,axis)[axis]/area_75+isoPrestress,
  })
plot.plot(subPlots=False)
#O.run()
initTest()
waitIfBatch()

vtkExporter.exportSpheres(what=dict(particleDisplacment='b.state.displ()'),useRef=True) <<

> I get a black output screen

while terminal prints "No suitable packing in database found, running PERIODIC compression"?
If so, you have to wait, or set spheresInCell to a lower value, e.g. 500

> vtkExporter = export.VTKExporter('baseFileName')

you will get
NameError: name 'export' is not defined

> vtkExporter.exportSpheres(what=dict(particleDisplacment='b.state.displ()'),useRef=True) <<

as it is, it saves initial state (zero displacement).
If you want to see progress, use it inside a PyRunner or after something like O.wait()

Cheers
Jan