No visualisation of Paraview

Asked by Temitope on 2017-04-27

Hi there,

Please I am modifying the rot_compress.py tutorial to do the post processing of the result in Paraview. However, nothing was displayed for the paraview. Please help . Here is the response from the command page and the code

 adminuser@temitope-oladele:~$ export PATH=/usr/local/bin/:$PATH
adminuser@temitope-oladele:~$ export LD_LIBRARY_PATH=/usr/local/lib/:$LD_LIBRARY_PATH
adminuser@temitope-oladele:~$ export LIBRARY_PATH=/usr/local/lib/:$LIBRARY_PATH
adminuser@temitope-oladele:~$ export PYTHONPATH=/usr/local/lib/python2.7/dist-packages/:$PYTHONPATH
adminuser@temitope-oladele:~$ mpirun -np 2 esysparticle rot_compress.py
CSubLatticeControler::initMPI()
slave started at local/global rank 0 / 1
constructing FieldMaster for field e_kin
constructing FieldMaster for field potential_energy
constructing FieldMaster for field count
constructing FieldMaster for field Position
constructing FieldMaster for field Force
adminuser@temitope-oladele:~$ dump2vtk -i snapshot -o vtk_snaps_ -rot -t 0 251 1000
version : 3
infilename : snapshot_t=0_0.txt
nr. of filenames: 1
snapshot_t=0_1.txt , 1
version : 3
infilename : snapshot_t=1000_0.txt
nr. of filenames: 1
snapshot_t=1000_1.txt , 1
version : 3
infilename : snapshot_t=2000_0.txt
nr. of filenames: 1
snapshot_t=2000_1.txt , 1
version : 3
infilename : snapshot_t=3000_0.txt
nr. of filenames: 1
snapshot_t=3000_1.txt , 1
version : 3
infilename : snapshot_t=4000_0.txt
nr. of filenames: 1
snapshot_t=4000_1.txt , 1
version : 3
infilename : snapshot_t=5000_0.txt
nr. of filenames: 1
snapshot_t=5000_1.txt , 1
version : 3
infilename : snapshot_t=6000_0.txt
nr. of filenames: 1
snapshot_t=6000_1.txt , 1
version : 3
infilename : snapshot_t=7000_0.txt
nr. of filenames: 1
snapshot_t=7000_1.txt , 1
version : 3
infilename : snapshot_t=8000_0.txt
nr. of filenames: 1
snapshot_t=8000_1.txt , 1
version : 3
infilename : snapshot_t=9000_0.txt
nr. of filenames: 1
snapshot_t=9000_1.txt , 1
version : 3
infilename : snapshot_t=10000_0.txt
nr. of filenames: 1
snapshot_t=10000_1.txt , 1
version : 3
infilename : snapshot_t=11000_0.txt
nr. of filenames: 1
snapshot_t=11000_1.txt , 1
version : 3
infilename : snapshot_t=12000_0.txt
nr. of filenames: 1
snapshot_t=12000_1.txt , 1
version : 3
infilename : snapshot_t=13000_0.txt
nr. of filenames: 1
snapshot_t=13000_1.txt , 1
version : 3
infilename : snapshot_t=14000_0.txt
nr. of filenames: 1
snapshot_t=14000_1.txt , 1
version : 3
infilename : snapshot_t=15000_0.txt
nr. of filenames: 1
snapshot_t=15000_1.txt , 1
version : 3
infilename : snapshot_t=16000_0.txt
nr. of filenames: 1
snapshot_t=16000_1.txt , 1
version : 3
infilename : snapshot_t=17000_0.txt
nr. of filenames: 1
snapshot_t=17000_1.txt , 1
version : 3
infilename : snapshot_t=18000_0.txt
nr. of filenames: 1
snapshot_t=18000_1.txt , 1
version : 3
infilename : snapshot_t=19000_0.txt
nr. of filenames: 1
snapshot_t=19000_1.txt , 1
version : 3
infilename : snapshot_t=20000_0.txt
nr. of filenames: 1
snapshot_t=20000_1.txt , 1
version : 3
infilename : snapshot_t=21000_0.txt
nr. of filenames: 1
snapshot_t=21000_1.txt , 1
version : 3
infilename : snapshot_t=22000_0.txt
nr. of filenames: 1
snapshot_t=22000_1.txt , 1
version : 3
infilename : snapshot_t=23000_0.txt
nr. of filenames: 1
snapshot_t=23000_1.txt , 1
version : 3
infilename : snapshot_t=24000_0.txt
nr. of filenames: 1
snapshot_t=24000_1.txt , 1
version : 3
infilename : snapshot_t=25000_0.txt
nr. of filenames: 1
snapshot_t=25000_1.txt , 1
version : 3
infilename : snapshot_t=26000_0.txt
nr. of filenames: 1
snapshot_t=26000_1.txt , 1
version : 3
infilename : snapshot_t=27000_0.txt
nr. of filenames: 1
snapshot_t=27000_1.txt , 1
version : 3
infilename : snapshot_t=28000_0.txt
nr. of filenames: 1
snapshot_t=28000_1.txt , 1
version : 3
infilename : snapshot_t=29000_0.txt
nr. of filenames: 1
snapshot_t=29000_1.txt , 1
version : 3
infilename : snapshot_t=30000_0.txt
nr. of filenames: 1
snapshot_t=30000_1.txt , 1
version : 3
infilename : snapshot_t=31000_0.txt
nr. of filenames: 1
snapshot_t=31000_1.txt , 1
version : 3
infilename : snapshot_t=32000_0.txt
nr. of filenames: 1
snapshot_t=32000_1.txt , 1
version : 3
infilename : snapshot_t=33000_0.txt
nr. of filenames: 1
snapshot_t=33000_1.txt , 1
version : 3
infilename : snapshot_t=34000_0.txt
nr. of filenames: 1
snapshot_t=34000_1.txt , 1
version : 3
infilename : snapshot_t=35000_0.txt
nr. of filenames: 1
snapshot_t=35000_1.txt , 1
version : 3
infilename : snapshot_t=36000_0.txt
nr. of filenames: 1
snapshot_t=36000_1.txt , 1
version : 3
infilename : snapshot_t=37000_0.txt
nr. of filenames: 1
snapshot_t=37000_1.txt , 1
version : 3
infilename : snapshot_t=38000_0.txt
nr. of filenames: 1
snapshot_t=38000_1.txt , 1
version : 3
infilename : snapshot_t=39000_0.txt
nr. of filenames: 1
snapshot_t=39000_1.txt , 1
version : 3
infilename : snapshot_t=40000_0.txt
nr. of filenames: 1
snapshot_t=40000_1.txt , 1
version : 3
infilename : snapshot_t=41000_0.txt
nr. of filenames: 1
snapshot_t=41000_1.txt , 1
version : 3
infilename : snapshot_t=42000_0.txt
nr. of filenames: 1
snapshot_t=42000_1.txt , 1
version : 3
infilename : snapshot_t=43000_0.txt
nr. of filenames: 1
snapshot_t=43000_1.txt , 1
version : 3
infilename : snapshot_t=44000_0.txt
nr. of filenames: 1
snapshot_t=44000_1.txt , 1
version : 3
infilename : snapshot_t=45000_0.txt
nr. of filenames: 1
snapshot_t=45000_1.txt , 1
version : 3
infilename : snapshot_t=46000_0.txt
nr. of filenames: 1
snapshot_t=46000_1.txt , 1
version : 3
infilename : snapshot_t=47000_0.txt
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snapshot_t=47000_1.txt , 1
version : 3
infilename : snapshot_t=48000_0.txt
nr. of filenames: 1
snapshot_t=48000_1.txt , 1
version : 3
infilename : snapshot_t=49000_0.txt
nr. of filenames: 1
snapshot_t=49000_1.txt , 1
version : 3
infilename : snapshot_t=50000_0.txt
nr. of filenames: 1
snapshot_t=50000_1.txt , 1
version : 3
infilename : snapshot_t=51000_0.txt
nr. of filenames: 1
snapshot_t=51000_1.txt , 1
version : 3
infilename : snapshot_t=52000_0.txt
nr. of filenames: 1
snapshot_t=52000_1.txt , 1
version : 3
infilename : snapshot_t=53000_0.txt
nr. of filenames: 1
snapshot_t=53000_1.txt , 1
version : 3
infilename : snapshot_t=54000_0.txt
nr. of filenames: 1
snapshot_t=54000_1.txt , 1
version : 3
infilename : snapshot_t=55000_0.txt
nr. of filenames: 1
snapshot_t=55000_1.txt , 1
version : 3
infilename : snapshot_t=56000_0.txt
nr. of filenames: 1
snapshot_t=56000_1.txt , 1
version : 3
infilename : snapshot_t=57000_0.txt
nr. of filenames: 1
snapshot_t=57000_1.txt , 1
version : 3
infilename : snapshot_t=58000_0.txt
nr. of filenames: 1
snapshot_t=58000_1.txt , 1
version : 3
infilename : snapshot_t=59000_0.txt
nr. of filenames: 1
snapshot_t=59000_1.txt , 1
version : 3
infilename : snapshot_t=60000_0.txt
nr. of filenames: 1
snapshot_t=60000_1.txt , 1
version : 3
infilename : snapshot_t=61000_0.txt
nr. of filenames: 1
snapshot_t=61000_1.txt , 1
version : 3
infilename : snapshot_t=62000_0.txt
nr. of filenames: 1
snapshot_t=62000_1.txt , 1
version : 3
infilename : snapshot_t=63000_0.txt
nr. of filenames: 1
snapshot_t=63000_1.txt , 1
version : 3
infilename : snapshot_t=64000_0.txt
nr. of filenames: 1
snapshot_t=64000_1.txt , 1
version : 3
infilename : snapshot_t=65000_0.txt
nr. of filenames: 1
snapshot_t=65000_1.txt , 1
version : 3
infilename : snapshot_t=66000_0.txt
nr. of filenames: 1
snapshot_t=66000_1.txt , 1
version : 3
infilename : snapshot_t=67000_0.txt
nr. of filenames: 1
snapshot_t=67000_1.txt , 1
version : 3
infilename : snapshot_t=68000_0.txt
nr. of filenames: 1
snapshot_t=68000_1.txt , 1
version : 3
infilename : snapshot_t=69000_0.txt
nr. of filenames: 1
snapshot_t=69000_1.txt , 1
version : 3
infilename : snapshot_t=70000_0.txt
nr. of filenames: 1
snapshot_t=70000_1.txt , 1
version : 3
infilename : snapshot_t=71000_0.txt
nr. of filenames: 1
snapshot_t=71000_1.txt , 1
version : 3
infilename : snapshot_t=72000_0.txt
nr. of filenames: 1
snapshot_t=72000_1.txt , 1
version : 3
infilename : snapshot_t=73000_0.txt
nr. of filenames: 1
snapshot_t=73000_1.txt , 1
version : 3
infilename : snapshot_t=74000_0.txt
nr. of filenames: 1
snapshot_t=74000_1.txt , 1
version : 3
infilename : snapshot_t=75000_0.txt
nr. of filenames: 1
snapshot_t=75000_1.txt , 1
version : 3
infilename : snapshot_t=76000_0.txt
nr. of filenames: 1
snapshot_t=76000_1.txt , 1
version : 3
infilename : snapshot_t=77000_0.txt
nr. of filenames: 1
snapshot_t=77000_1.txt , 1
version : 3
infilename : snapshot_t=78000_0.txt
nr. of filenames: 1
snapshot_t=78000_1.txt , 1
version : 3
infilename : snapshot_t=79000_0.txt
nr. of filenames: 1
snapshot_t=79000_1.txt , 1
version : 3
infilename : snapshot_t=80000_0.txt
nr. of filenames: 1
snapshot_t=80000_1.txt , 1
version : 3
infilename : snapshot_t=81000_0.txt
nr. of filenames: 1
snapshot_t=81000_1.txt , 1
version : 3
infilename : snapshot_t=82000_0.txt
nr. of filenames: 1
snapshot_t=82000_1.txt , 1
version : 3
infilename : snapshot_t=83000_0.txt
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snapshot_t=83000_1.txt , 1
version : 3
infilename : snapshot_t=84000_0.txt
nr. of filenames: 1
snapshot_t=84000_1.txt , 1
version : 3
infilename : snapshot_t=85000_0.txt
nr. of filenames: 1
snapshot_t=85000_1.txt , 1
version : 3
infilename : snapshot_t=86000_0.txt
nr. of filenames: 1
snapshot_t=86000_1.txt , 1
version : 3
infilename : snapshot_t=87000_0.txt
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snapshot_t=87000_1.txt , 1
version : 3
infilename : snapshot_t=88000_0.txt
nr. of filenames: 1
snapshot_t=88000_1.txt , 1
version : 3
infilename : snapshot_t=89000_0.txt
nr. of filenames: 1
snapshot_t=89000_1.txt , 1
version : 3
infilename : snapshot_t=90000_0.txt
nr. of filenames: 1
snapshot_t=90000_1.txt , 1
version : 3
infilename : snapshot_t=91000_0.txt
nr. of filenames: 1
snapshot_t=91000_1.txt , 1
version : 3
infilename : snapshot_t=92000_0.txt
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version : 3
infilename : snapshot_t=93000_0.txt
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version : 3
infilename : snapshot_t=94000_0.txt
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version : 3
infilename : snapshot_t=95000_0.txt
nr. of filenames: 1
snapshot_t=95000_1.txt , 1
version : 3
infilename : snapshot_t=96000_0.txt
nr. of filenames: 1
snapshot_t=96000_1.txt , 1
version : 3
infilename : snapshot_t=97000_0.txt
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version : 3
infilename : snapshot_t=98000_0.txt
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version : 3
infilename : snapshot_t=99000_0.txt
nr. of filenames: 1
snapshot_t=99000_1.txt , 1
version : 3
infilename : snapshot_t=100000_0.txt
nr. of filenames: 1
snapshot_t=100000_1.txt , 1
version : 3
infilename : snapshot_t=101000_0.txt
nr. of filenames: 1
snapshot_t=101000_1.txt , 1
version : 3
infilename : snapshot_t=102000_0.txt
nr. of filenames: 1
snapshot_t=102000_1.txt , 1
version : 3
infilename : snapshot_t=103000_0.txt
nr. of filenames: 1
snapshot_t=103000_1.txt , 1
version : 3
infilename : snapshot_t=104000_0.txt
nr. of filenames: 1
snapshot_t=104000_1.txt , 1
version : 3
infilename : snapshot_t=105000_0.txt
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version : 3
infilename : snapshot_t=106000_0.txt
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version : 3
infilename : snapshot_t=107000_0.txt
nr. of filenames: 1
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version : 3
infilename : snapshot_t=108000_0.txt
nr. of filenames: 1
snapshot_t=108000_1.txt , 1
version : 3
infilename : snapshot_t=109000_0.txt
nr. of filenames: 1
snapshot_t=109000_1.txt , 1
version : 3
infilename : snapshot_t=110000_0.txt
nr. of filenames: 1
snapshot_t=110000_1.txt , 1
version : 3
infilename : snapshot_t=111000_0.txt
nr. of filenames: 1
snapshot_t=111000_1.txt , 1
version : 3
infilename : snapshot_t=112000_0.txt
nr. of filenames: 1
snapshot_t=112000_1.txt , 1
version : 3
infilename : snapshot_t=113000_0.txt
nr. of filenames: 1
snapshot_t=113000_1.txt , 1
version : 3
infilename : snapshot_t=114000_0.txt
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snapshot_t=114000_1.txt , 1
version : 3
infilename : snapshot_t=115000_0.txt
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version : 3
infilename : snapshot_t=116000_0.txt
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version : 3
infilename : snapshot_t=117000_0.txt
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snapshot_t=117000_1.txt , 1
version : 3
infilename : snapshot_t=118000_0.txt
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version : 3
infilename : snapshot_t=119000_0.txt
nr. of filenames: 1
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version : 3
infilename : snapshot_t=120000_0.txt
nr. of filenames: 1
snapshot_t=120000_1.txt , 1
version : 3
infilename : snapshot_t=121000_0.txt
nr. of filenames: 1
snapshot_t=121000_1.txt , 1
version : 3
infilename : snapshot_t=122000_0.txt
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version : 3
infilename : snapshot_t=123000_0.txt
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snapshot_t=123000_1.txt , 1
version : 3
infilename : snapshot_t=124000_0.txt
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version : 3
infilename : snapshot_t=125000_0.txt
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infilename : snapshot_t=126000_0.txt
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infilename : snapshot_t=127000_0.txt
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version : 3
infilename : snapshot_t=128000_0.txt
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version : 3
infilename : snapshot_t=129000_0.txt
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version : 3
infilename : snapshot_t=130000_0.txt
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version : 3
infilename : snapshot_t=131000_0.txt
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infilename : snapshot_t=132000_0.txt
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infilename : snapshot_t=133000_0.txt
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infilename : snapshot_t=159000_0.txt
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infilename : snapshot_t=160000_0.txt
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Code:

#import the approprate esysparticle modules
from esys.lsm import*
from esys.lsm.util import*
from esys.lsm.geometry import*
from WallLoader import WallLoaderRunnable

#instantiate a simulation object
sim = LsmMpi (numWorkerProcesses = 1, mpiDimList = [1,1,1])

#initialise the neighbouring search algorithm
sim.initNeighbourSearch (
 particleType = "RotSphere",
 gridSpacing = 5.0000,
 verletDist = 0.08000
)

#set the number of timesteps and timestep increament:
sim.setNumTimeSteps (250000)
sim.setTimeStepSize (1.0000e-06)

#specify the spatial domain for the simulation
domain = BoundingBox(Vec3(-20,-20,20), Vec3(20,20,20))
sim.setSpatialDomain (domain)

#create a prism of speherical particles
geoRandomBlock = RandomBoxPacker (
 minRadius = 0.400,
 maxRadius = 2.0000,
 cubicPackRadius = 2.2000,
 maxInsertFails = 5000,
 bBox = BoundingBox(
  Vec3(-5.0000, 0.0000, -5.0000),
  Vec3(5.0000, 20.0000, 5.00000)
 ),
 circDimList = [False, False, False],
 tolerance = 1.0000e-05
)
geoRandomBlock.generate()
geoRandomBlock_particles = geoRandomBlock.getSimpleSphereCollection()

#add the particles to the simulation object:
sim.createParticles(geoRandomBlock_particles)

#bond particles together with bondTag =1:
sim.createConnections(
 ConnectionFinder(
  maxDist = 0.005,
  bondTag = 1,
  pList = geoRandomBlock_particles
 )
)

#Create bottom wall of the come.
sim.createWall (
 name = "bottom_wall",
 posn = Vec3(0.0000, 0.0000, 0.0000),
 normal = Vec3(0.0000, 1.0000, 0.0000)
)

#create a wall at the top of the model:
sim.createWall (
 name = "top_wall",
 posn = Vec3(0.0000, 20.0000, 0.0000),
 normal = Vec3(0.0000, -1.0000, 0.0000)
)
#specify elastic repulsion from the bottom wall:
sim.createInteractionGroup (
 NRotElasticWallPrms (
  name = "bottom_wall_repel",
  wallName = "bottom_wall",
  normalK = 100000.0
 )
)

#Specify elastic repulsion from topwall:
sim.createInteractionGroup (
 NRotElasticWallPrms (
  name = "top_wall_repel",
  wallName = "top_wall",
  normalK = 100000.0
 )
)
#create rotational elastic-brittle bonds between particles:
pp_bonds = sim.createInteractionGroup (
 BrittleBeamPrms(
  name="pp_bonds",
  youngsModulus=100000.0,
  poissonsRatio=0.25,
  cohesion=100.0,
  tanAngle=1.0,
  tag=1
 )
)
#initialise frictional interactions for unbonded particles:
sim.createInteractionGroup (
 FrictionPrms(
  name="friction",
  youngsModulus=100000.0,
  poissonsRatio=0.25,
  dynamicMu=0.4,
  staticMu=0.6
 )
)
#create an exlusion between particle pair i.e there undergo bonded or frictional interaction but not both
sim.createExclusion (
 interactionName1 ="pp_bonds",
 interactionName2 = "friction"
)
#add translational viscous damping:
sim.createInteractionGroup (
 LinDampingPrms(
  name="damping1",
  viscosity=0.002,
  maxIterations=50
 )
)
#add rotational viscous damping:
sim.createInteractionGroup (
 RotDampingPrms(
  name="damping2",
  viscosity=0.002,
  maxIterations=50
 )
)

#add a wall loader to move the top wall:
wall_loader1 = WallLoaderRunnable (
 LsmMpi =sim,
 wallName = 'top_wall',
 vPlate = Vec3(0.0, -0.125, 0.0),
 startTime = 0,
 rampTime = 50000
)
sim.addPreTimeStepRunnable (wall_loader1)

#add a wall loader to move the bottom wall:
wall_loader2 = WallLoaderRunnable (
 LsmMpi = sim,
 wallName = "bottom_wall",
 vPlate = Vec3(0.0, 0.125, 0.0),
 startTime = 0,
 rampTime = 50000
)
sim.addPreTimeStepRunnable (wall_loader2)

#create a FiledSaver to store the total kinetic energy of the particles:
sim.createFieldSaver (
 ParticleScalarFieldSaverPrms(
  fieldName="e_kin",
  fileName="ekin.dat",
  fileFormat="SUM",
  beginTimeStep=0,
  endTimeStep=250000,
  timeStepIncr=1
 )
)

#create a FieldSaver to store potential energy stored in bonds:
sim.createFieldSaver(
 InteractionScalarFieldSaverPrms(
  interactionName="pp_bonds",
  fieldName="potential_energy",
  fileName="epot.dat",
  fileFormat="SUM",
  beginTimeStep=0,
  endTimeStep=250000,
  timeStepIncr=1
 )
)

#create a FieldSaver to store number of bonds:
sim.createFieldSaver(
 InteractionScalarFieldSaverPrms(
  interactionName="pp_bonds",
  fieldName="count",
  fileName="nbonds.dat",
  fileFormat="SUM",
  beginTimeStep=0,
  endTimeStep=250000,
  timeStepIncr=1
 )
)

#create a FieldSaver to wall positions:
posn_saver = WallVectorFieldSaverPrms(
 wallName=["bottom_wall", "top_wall"],
 fieldName="Position",
 fileName="out_Position.dat",
 fileFormat="RAW_SERIES",
 beginTimeStep=0,
 endTimeStep=250000,
 timeStepIncr = 10
)
sim.createFieldSaver(posn_saver)

#create FieldSaver to wall forces:
force_saver = WallVectorFieldSaverPrms(
 wallName=["bottom_wall", "top_wall"],
 fieldName="Force",
 fileName="out_Force.dat",
 fileFormat="RAW_SERIES",
 beginTimeStep=0,
 endTimeStep=250000,
 timeStepIncr=10
)
sim.createFieldSaver(force_saver)

sim.createCheckPointer (
 CheckPointPrms (
  fileNamePrefix = "snapshot",
  beginTimeStep = 0,
  endTimeStep = 250000,
  timeStepIncr = 1000
 )
)

#execute the simulation:
sim.run()

Question information

Language:
English Edit question
Status:
Answered
For:
ESyS-Particle Edit question
Assignee:
No assignee Edit question
Last query:
2017-04-27
Last reply:
2017-04-28
Qi Shao (uqqshao) said : #1

Hi Temitope,

Change "domain = BoundingBox(Vec3(-20,-20,20), Vec3(20,20,20))" to "domain = BoundingBox(Vec3(-20,-20,-20), Vec3(20,20,20))" in you script - you have missed a minus "-".

Cheers,
Qi

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