# Rotate cylinder

Hi,

How can I rotate this half cylinder 90 degrees in y-axis:

#Cylinderpunch
cyl1 = [f for f in cyl1 if f.state.pos < 0] # "half-cylinder"
cyl1=O.bodies.append(cyl1)

for j in cyl1:
body= O.bodies[j]
body.state.rot=(0,90,0)

I tried this, but it did not move my cylinder.

Here is my code:

#!/usr/bin/env python
#encoding: ascii

# Testing of the Deformation Enginge with Luding Contact Law
# Modified Oedometric Test

from yade import utils, plot, timing
import pandas as pd

o = Omega()

# Physical parameters
fr = 0.52
rho = 1050 #kg/m3
Diameter = 0.0079 #79 micrometer
r1 = Diameter
r2 = Diameter
k1 = 126000.0
kp = 12.0*k1
kc = k1 * 0.1
ks = k1 * 0.1
DeltaPMax = Diameter/3.0
Chi1 = 0.34

o.dt = 1.0e-5

particleMass = 4.0/3.0*math.pi*r1*r1*r1*rho

Vi1 = math.sqrt(k1/particleMass)*DeltaPMax*Chi1
PhiF1=0.999
#PhiF1 = DeltaPMax*(kp-k1)*(r1+r2)/(kp*2*r1*r2)

#*************************************

mat1 = O.materials.append(LudingMat(frictionAngle=fr, density=rho, k1=k1, kp=kp, ks=ks, kc=kc, PhiF=PhiF1, G0 = 0.0))

# Spheres for compression
# Spheres for compression

sp=pack.SpherePack()
sp.makeCloud((-9.5*Diameter,-9.5*Diameter,-35.0*Diameter),(9.5*Diameter,9.5*Diameter,15.0*Diameter), rMean=Diameter/2.0)

#Cylinder cloud sphere pack
cyl = pack.inCylinder((0,0,0),(0,0,20*Diameter),8*Diameter-0.006)
sp = pack.filterSpherePack(cyl,sp,True,material=mat1)
sp.toSimulation(material=mat1)

##No of particles
count = 0
for b in O.bodies:
if isinstance(b.shape, Sphere):
count +=1
##Mass of particles
n_p=count

######################################################################
#height=0.067
##Top punch##
#find max Z coordinate of your cloud
max_z = aabbExtrema()
min_z = aabbExtrema()

#Top_punch=O.bodies.append(wall((0,0,max_z), axis=2, sense=-1, material=mat1))
#O.bodies[Top_punch].state.vel = (0, 0, -0.01)

#Cylinderpunch
cyl1 = [f for f in cyl1 if f.state.pos < 0] # "half-cylinder"
cyl1=O.bodies.append(cyl1)

for j in cyl1:
body= O.bodies[j]
body.state.rot=(0,180,0)

for i in cyl1:
body= O.bodies[i]
body.state.vel = (0,1,0)

df = pd.DataFrame(columns=['time','Porosity','Maxoverlap','Stress'])
df.to_csv('PH101_Gao_speed_5.csv')
from csv import writer
def append_list_as_row(file_name, list_of_elem):
# Open file in append mode
with open(file_name, 'a+', newline='') as write_obj:
# Create a writer object from csv module
csv_writer = writer(write_obj)
# Add contents of list as last row in the csv file
csv_writer.writerow(list_of_elem)

o.engines = [
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1.05),
Bo1_Wall_Aabb(),
Bo1_Facet_Aabb()
]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1.05),
Ig2_Facet_Sphere_ScGeom(),
Ig2_Wall_Sphere_ScGeom()],
[Ip2_LudingMat_LudingMat_LudingPhys()],
[Law2_ScGeom_LudingPhys_Basic()]
),
NewtonIntegrator(damping=0.1, gravity=[0, 0, -9.81]),
#VTKRecorder(fileName='vtk-',recorders=['all'],iterPeriod=10000),
#PyRunner(command='checkForce()', realPeriod=1, label="fCheck"),
#PyRunner(command='print(voxelPorosity(resolution=600,start=aabbExtrema(),end=aabbExtrema()))', realPeriod=15),
PyRunner(command='checkdata()', realPeriod=3),
PyRunner(command='checkForce()', realPeriod=1, label="fCheck"),
DeformControl(label="DefControl")
]

def checkdata():
if O.iter < 20000:
return
else:
time=o.realtime
porosity=voxelPorosity(resolution=600,start=aabbExtrema(),end=aabbExtrema())
Maxoverlap=utils.maxOverlapRatio()
stress=getStress().trace()/3.
row_contents = [time,time,porosity,Maxoverlap,stress]
append_list_as_row('PH101_Gao_speed_5.csv', row_contents)

def checkForce():
# at the very start, unbalanced force can be low as there is only few
# contacts, but it does not mean the packing is stable
if O.iter < 20000:
return
# the rest will be run only if unbalanced is < .1 (stabilized packing)
timing.reset()
if unbalancedForce() > 0.2:
return
# add plate at upper box side

highSphere = 0.0
for b in O.bodies:
if highSphere < b.state.pos and isinstance(b.shape, Sphere):
highSphere = b.state.pos
else:
pass

O.bodies.append(wall(highSphere+0.5*Diameter, axis=2, sense=-1, material=mat1))
# without this line, the plate variable would only exist inside this
# function
global plate
plate = O.bodies[-1] # the last particles is the plate
# Wall objects are "fixed" by default, i.e. not subject to forces
# prescribing a velocity will therefore make it move at constant velocity
# (downwards)
plate.state.vel = (0, 0, -0.01)

## Question information

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Jan Stránský
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Last query:
 Revision history for this message  Jan Stránský (honzik) said on 2021-03-26: #1

Hello,

> Here is my code:

most of the code is irrelevant to the problem.
Please try to create a MWE , M = minimal (unnecessary code removed, focusing on the problem)
Your "initial" code would be just fine (with "Diamater" variable defined), showing the entire problem ("I intended to rotate these bodies, but they are not rotated")
The rest just scares/discourages potential helpers :-)

state.rot is a method to get relative rotation from initial rotation , something like state.displ().
With your code, you just overwritten the method to the (0,90,0) tuple, try this:
###
Diameter = 0.0079 #79 micrometer
cyl1 = [f for f in cyl1 if f.state.pos < 0] # "half-cylinder"
cyl1=O.bodies.append(cyl1)

for j in cyl1:
body= O.bodies[j]
print(body.state.rot) # <bound method State.rot ...
body.state.rot=(0,90,0)
print(body.state.rot) # (0,90,0)
###

Just a note, in Yade the angles are rarely (if at all) in degrees..

To rotate a body, you have to modify state.ori. If the center of rotation is not state.pos, you have to modify state.pos as well:
###
Diameter = 0.0079 #79 micrometer
cyl1 = [f for f in cyl1 if f.state.pos < 0] # "half-cylinder"
cyl1=O.bodies.append(cyl1)

rot = Quaternion((0,0,1),.5*pi) # 90 degrees around z axis
center = Vector3(0,0,0) # center of rotation

for j in cyl1:
body= O.bodies[j]
# change rotation
body.state.ori *= rot
# shift the body
p = body.state.pos - center # relative vector from center to pos
p = rot * p # rotated relative vector
body.state.pos = center + p # new pos
###

cheers
Jan

 Revision history for this message Jérôme Duriez (jduriez) said on 2021-03-26: #2

Depending on your needs (change the default initial orientation by a 90 degrees rotation, or impose a gradual rotation up to 90 degrees), it is a good YADE habit (for the 2nd case) to go through angular velocities, resp. velocities, and not update directly orientation, resp. position.
See https://yade-dem.org/doc/user.html#imposed-velocity (the same may apply for angular velocities and orientation)

 Revision history for this message Mithushan Soundaranathan (mithushan93) said on 2021-03-30: #3

Thanks Jan Stránský, that solved my question.