Re: [Paraview] Error reading timeseries with spatial grid collection with XDMF
I tried reading them with XDMF 3 reader and it works fine. Thank you for the suggestions. Nikos On Mon, Nov 20, 2017 at 2:14 PM, David E DeMarle wrote: > It might be that the reader doesn't like or want that both of your times > are 0.0. > ... > > ... > > ... > but your third case doesn't fit that hypothesis. > > Otherwise your file looks ok at first glance. I'ld have to debug the > reader on your data to figure out what is going wrong. > > David E DeMarle > Kitware, Inc. > Principal Engineer > 21 Corporate Drive > <https://maps.google.com/?q=21+Corporate+Drive+Clifton+Park,+NY+12065&entry=gmail&source=g> > Clifton Park, NY 12065 > <https://maps.google.com/?q=21+Corporate+Drive+Clifton+Park,+NY+12065&entry=gmail&source=g> > -8662 > Phone: 518-881-4909 <(518)%20881-4909> > > On Sun, Nov 12, 2017 at 11:15 PM, Joachim Pouderoux < > joachim.pouder...@kitware.com> wrote: > >> Nikos, >> >> It looks like you are using the Xdmf2 based reader. >> Did you give a chance to the one based on Xdmf3? >> What version of ParaView are you using? >> Can you provide a full dataset we could use to reproduce the issue? >> >> Best, >> >> >> *Joachim Pouderoux*, PhD >> >> *Technical Expert - Scientific Computing Team* >> *Kitware SAS <http://www.kitware.fr>* >> >> >> 2017-11-11 19:31 GMT+01:00 Nikolaos Beratlis : >> >>> Hi, >>> >>> I have a cartesian structured grid made of two sub-domains and a two >>> snap shots in a time that I would like to read in Paraview. The data and >>> grid files are stored in HDF5 file and I use a XDMF file to read them in a >>> Paraview. The XDMF files looks like this: >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001 >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/YC >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001 >>> >>> >>> >>> >> Format="HDF"> >>> ../Q_VPreg.h5sp.0001:/zone0001 >>> >>> >>> >>> >>> >>> >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002 >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/YC >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002 >>> >>> >>> >>> >> Format="HDF"> >>> ../Q_VPreg.h5sp.0001:/zone0002 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001 >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/YC >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001 >>> >>> >>> >>> >> Format="HDF"> >>> ../Q_VPreg.h5sp.0001:/zone0001 >>> >>> >>> >>> >>> >>> >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002 >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/YC >>> >>> >> Format="HDF"> >>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002 >>> >>> >>> >>> >> Format="HDF"> >>> ../Q_VPreg.h5sp.0002:/zone0002 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> The file is read in Paraview. When I advance in to the second instant in >>> time I get the following error: >>> >>> Failed to read attribute data. >>> >>> Paraview shows data from the first subset (zone0001), it can't read the >>> data from the second subset (zone0002). >>> >>> >>> When I read only on instant in time like this: >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> &
[Paraview] Error reading timeseries with spatial grid collection with XDMF
Hi, I have a cartesian structured grid made of two sub-domains and a two snap shots in a time that I would like to read in Paraview. The data and grid files are stored in HDF5 file and I use a XDMF file to read them in a Paraview. The XDMF files looks like this: ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001 ../grid_VPreg_vxvyvz.h5sp:/YC ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001 ../Q_VPreg.h5sp.0001:/zone0001 ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002 ../grid_VPreg_vxvyvz.h5sp:/YC ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002 ../Q_VPreg.h5sp.0001:/zone0002 ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001 ../grid_VPreg_vxvyvz.h5sp:/YC ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001 ../Q_VPreg.h5sp.0001:/zone0001 ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002 ../grid_VPreg_vxvyvz.h5sp:/YC ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002 ../Q_VPreg.h5sp.0002:/zone0002 The file is read in Paraview. When I advance in to the second instant in time I get the following error: Failed to read attribute data. Paraview shows data from the first subset (zone0001), it can't read the data from the second subset (zone0002). When I read only on instant in time like this: ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001 ../grid_VPreg_vxvyvz.h5sp:/YC ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001 ../Q_VPreg.h5sp.0001:/zone0001 ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002 ../grid_VPreg_vxvyvz.h5sp:/YC ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002 ../Q_VPreg.h5sp.0001:/zone0002 the file is read successfully and no errors show up. Also when I read two time instants but with only one subset (zone0001) Paraview doesn't throw any errors. ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001 ../grid_VPreg_vxvyvz.h5sp:/YC ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001 ../Q_VPreg.h5sp.0001:/zone0001 ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001 ../grid_VPreg_vxvyvz.h5sp:/YC ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001 ../Q_VPreg.h5sp.0001:/zone0001 Does anyone see the problem in the code? Kind regards, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] Error reading XDMF file
Hi, I have the following XDMF file: http://www.w3.org/2003/XInclude"; Version="2.0"> ../grid3dc_vxvyvz_VP.h5sp:/X ../grid3dc_vxvyvz_VP.h5sp:/Y ../grid3dc_vxvyvz_VP.h5sp:/Z ../Qcrit.0001.h5sp:/var3d I can read the file into Paraview 5.0 without any problems. When I try to read it with Paraview 4.1 I get the following error message: ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/Xdmf2/vtkXdmfHeavyData.cxx, line 1126 vtkXdmfReader (0x1177e62f0): Failed to read attribute data It seems that Paraview 4.1 reads the grid fine but it can't read the attribute. Any idea what is wrong? Regards, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] Reading a vector with XDMF and structured grid
Hi, I am trying to read a vector on a cartesian structured grid from 3 separate scalar variables as follows: http://www.w3.org/2003/XInclude"; Version="2.2"> ../grid3dc_vxvyvz_phavg.h5sp:/X ../grid3dc_vxvyvz_phavg.h5sp:/Y ../grid3dc_vxvyvz_phavg.h5sp:/Z ../uc_phavg.0001.h5sp:/var3d ../vc_phavg.0001.h5sp:/var3d ../wc_phavg.0001.h5sp:/var3d Paraview crashes. Is this the right way to read a vector from 3 separate files? Regards, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] Help with adjusting contour levels in python script
Hi, I am running a small python code with pvbatch that read a XDMF file and plots contours: cf_VP_anim_xmf = XDMFReader( FileName=wdir+'VPfield_files/XDMF/cf_VP' +index[i]+'.xmf' ) cf_VP_anim_xmf.CellArrays = [] cf_VP_anim_xmf.Sets = [] cf_VP_anim_xmf.PointArrays = ['Cf'] RenderView1 = GetRenderView() a1_Cf_PVLookupTable = GetLookupTableForArray( "Cf", 1 ) Cfcontours = Show() Cfcontours.EdgeColor = [0.0, 0.0, 0.5762951094835] Cfcontours.SelectionPointFieldDataArrayName = 'Cf' Cfcontours.ScalarOpacityFunction = [] Cfcontours.ColorArrayName = 'Cf' Cfcontours.ScalarOpacityUnitDistance = 2.4071425938556859 Cfcontours.LookupTable = a1_Cf_PVLookupTable Cfcontours.ScaleFactor = 15.0 cf_VP_anim_xmf.Grids = ['STL Grid'] RenderView1.CacheKey = 2.0 RenderView1.CameraClippingRange = [288.47079837284241, 299.16435388730815] RenderView1.UseCache = 0 a1_Cf_PVLookupTable = GetLookupTableForArray( "Cf", 1, RGBPoints=[- 0.0001, 0.0, 0.0, 1.0, 0.0001, 1.0, 0.0, 0.0], LockScalarRange=1, ColorSpace='HSV' ) separationline = Contour( PointMergeMethod="Uniform Binning" ) separationline.ContourBy = ['POINTS', 'Cf'] separationline.Isosurfaces = [0.0] DataSeparationLine = Show() DataSeparationLine.ScaleFactor = 12.321390008926393 DataSeparationLine.SelectionPointFieldDataArrayName = 'Cf' DataSeparationLine.EdgeColor = [0.0, 0.0, 0.5762951094835] DataSeparationLine.LineWidth = 2.0 DataSeparationLine.DiffuseColor = [0.0, 0.0, 0.0] DataSeparationLine.ColorArrayName = '' Cfcontours.Visibility = 1 #--- Setup view RenderView1 = GetRenderView() RenderView1.Background = [1.0, 1.0, 1.0] RenderView1.CenterAxesVisibility = 0 RenderView1.OrientationAxesVisibility = 0 RenderView1.ViewSize = [1450, 300] RenderView1.InteractionMode = '3D' RenderView1.CameraClippingRange = [120.40716073726786, 126.85668499830999] RenderView1.CameraPosition = [25.95, 41.63, 1.43] RenderView1.CameraFocalPoint = [4.31, 5.36, 4.77] RenderView1.CameraViewUp = [0.93, -0.36, -0.053] #--- Uncomment for 2D Interaction Mode #RenderView1.CameraParallelScale = 5.5 a1_Cf_PVLookupTable = GetLookupTableForArray( "Cf", 1, RGBPoints=[- 0.0001, 0.0, 0.0, 1.0, 0.0001, 1.0, 0.0, 0.0], LockScalarRange=1 ) #--- Export image Render() WriteImage(wdir+'POSTPRO/IMAGES/cf_view1_'+index[i]+'.jpg') I set the range of the contours from -0.0001 to 0.0001 but the contours levels revert back to automatic scaling instead of the range that I specify. I am using version 3.98 of Paraview but I also tried with version 4.1.0. Why is this happening? Do I miss something in my script? Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] How to change background color on scatter plot?
I have a scatter plot like this one and I want to change the background color from white to green or some other color. How can I do that? Regards, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] XY plot of time series
Hi, I am trying to create a plot of a time series. I read one file (0001) as follows: http://www.w3.org/2003/XInclude"; Version="2.2"> ../VPfield_files/grid3dc_vxvyvz_VP.h5sp:/X ../VPfield_files/grid3dc_vxvyvz_VP.h5sp:/Y ../VPfield_files/grid3dc_vxvyvz_VP.h5sp:/Z ../VPfield_files/ufluct.0001.h5sp:/var3d ../VPfield_files/wfluct.0001.h5sp:/var3d and I create a XY plot of the data as shown below: I want to superimpose on the same plot the data from the other files (0002-0025). Because the grid files are large and there are many files in the series I would like to do it without loading all the data simultaneously because I would ran out of memory. Is there a way to do this efficiently? Regards, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] Attribute recalculation at center
HI, I have a cartesian grid which I read into paraview along with its attribute as follows: http://www.w3.org/2003/XInclude"; Version="2.2"> ../grid3dc_vxvyvz_VP.h5sp:/X ../grid3dc_vxvyvz_VP.h5sp:/Y ../grid3dc_vxvyvz_VP.h5sp:/Z ../u_tmavg_cyl2car.h5sp:/var3d ../w_tmavg_cyl2car.h5sp:/var3d The variables are 3D arrays of size 202 x 100 x 100 (NZ x NY x NX). I want to create new variables as: do k=2,NZ do j=1,NY do i=1,NX Wnew(i,j,k) = 0.5*( W(i,j,k-1) + W(i,j,k) ) enddo enddo enddo and do k=1,NZ do j=1,NY do i=2,NX Unew(i,j,k) = 0.5*( U(i-1,j,k) + U(i,j,k) ) enddo enddo enddo I try to use the calculator filter but there is no option to specify the indices. How can I do that within Paraview? ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] Help with producing a X Y plot of a scalar
Hi, I have a cartesian grid and two scalars U, W that I read into paraview as follows: http://www.w3.org/2003/XInclude"; Version="2.2"> ../grid3dc_vxvyvz_VP.h5sp:/X ../grid3dc_vxvyvz_VP.h5sp:/Y ../grid3dc_vxvyvz_VP.h5sp:/Z ../oy_tmavg_cyl2car.h5sp:/var3d ../oy_tmavg_cyl2car.h5sp:/var3d I then multiply U*W using the calculator to get a new variable UW. What I want to do is create a scatter plot of the variable UW at a particular a slice in the domain where in the X-axis I have U variable and in the Y-axis I have W variable. The end result would like this Paraview has a function called scatter plot but it only allows to specify one axis, the X-axis data. How can I specify the Y-axis to be a different variable? Regards, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] Help with memory crash?
After reading about memory leaks I modified the script at the end by adding
"del" after "Delete":
Delete(DataRepresentation4)
del DataRepresentation4
Delete(Contour2)
del Contour2
Delete(DataRepresentation3)
del DataRepresentation3
Delete(Q_VP_xmf)
del Q_VP_xmf
Delete(DataRepresentation2)
del DataRepresentation2
Delete(Contour1)
del Contour1
Delete(DataRepresentation1)
del DataRepresentation1
Delete(cf_VP_xmf)
del cf_VP_xmf
That should fully delete the objects from the memory and it helped a little
but I still have memory leaks. Before the script memory usage in the Memory
Inspector is 1.4Gb and after one iteration it increases to 4Gb, compared to
10Gb without the del statements. After 4 iterations the memory usage
increases to 8Gb. Any ideas on how to track and eliminate completely the
memory leaks? I am forgetting to delete an object from the script?
On Wed, Jan 7, 2015 at 9:17 PM, Nikolaos Beratlis
wrote:
> So I did some more tests by running the script interactively. I used a
> smaller grid first, 2002 x 20 x 1000 points and ran it only for 1
> iteration. When Paraview loaded the memory usage on the server was 1.04GB.
> After doing one iteration the memory usage spiked to 10.42GB and remained
> like that when the script finished. What I found out is the Delete
> statements make no difference at all, with or without them the memory usage
> remained 10.42GB. Performing more iterations in the script actually worsens
> this problem, after 4 iterations the memory used increased to 14.32GB. With
> a larger grid of 2002 x 100 x 1000 points the memory after one iteration
> increased from 10.42GB before the script to 45.25GB after the script. How
> can I properly delete all datasets and clear the memory in Paraview?
>
>
>
> On Wed, Jan 7, 2015 at 2:55 PM, Nikolaos Beratlis <
> nikos.berat...@gmail.com> wrote:
>
>> I am trying to run a script on a cluster with Paraview in parallel. The
>> cluster architecture is 16cores and 64GB per node. The script reads in two
>> XMF files, one contains a grid of 2002x100x1000 points along with one
>> variable. There is a loop to perform two iterations:
>>
>> try: paraview.simple
>> except: from paraview.simple import *
>> paraview.simple._DisableFirstRenderCameraReset()
>>
>> RenderView1 = GetRenderView()
>> RenderView1.Background = [1.0, 1.0, 1.0]
>> view = GetActiveView()
>> view.ViewSize = [ 800, 500 ]
>>
>> RenderView1.CenterAxesVisibility = 0
>> #RenderView1.OrientationAxesVisibility = 0
>>
>> #Define variables
>> wdir =
>> '/lustre/groups/balarasgrp/nikosb/Research/Simulations/golfball/stationary/S120/Re20/gridC1/run_wm'
>> #wdir =
>> '/Users/nikosb/colone/Research/Simulations/golfball/stationary/S120/Re20/gridC1/run_wm'
>> #wdir = '/Users/nikosb/Research/Simulations/SPHERE/Re100/gridC1/run'
>> Qval = 0.1
>> cfmin = -0.001
>> cfmax = 0.005
>>
>> index = [None]*
>>
>> m = 0
>> for i in range(0, 9):
>> for j in range(0, 9):
>> for k in range(0, 9):
>> for l in range(0, 9):
>> index[m] = chr(i+48)+chr(j+48)+chr(k+48)+chr(l+48)
>> m = m+1
>>
>>
>> for i in range(1,3):
>>
>> cf_VP_xmf = XDMFReader(
>> FileName=wdir+'/VPfield/XDMF/cf_VP'+index[i]+'.xmf' )
>>
>> cf_VP_xmf.Sets = []
>> cf_VP_xmf.Grids = ['STL Grid']
>> cf_VP_xmf.PointArrays = ['Cf']
>>
>> RenderView1 = GetRenderView()
>> RenderView1.CenterOfRotation = [6.2286853790283203e-06,
>> 2.5033950805664062e-06, 7.1227550506591797e-06]
>>
>> DataRepresentation1 = Show()
>> DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5762951094835]
>> DataRepresentation1.SelectionPointFieldDataArrayName = 'Cf'
>> DataRepresentation1.ColorArrayName = ('POINT_DATA', 'Cf')
>> DataRepresentation1.ScalarOpacityUnitDistance = 0.03392870483226
>> DataRepresentation1.ScaleFactor = 0.08557567596444
>>
>> a1_Cf_PVLookupTable = GetLookupTableForArray( "Cf", 1,
>> RGBPoints=[-0.0099065126851201057, 0.23001,
>> 0.29899, 0.754, 0.0097341262735426426, 0.86499,
>> 0.86499, 0.86499, 0.029374765232205391,
>> 0.70596, 0.016, 0.14999], VectorMode='Magnitude',
>> NanColor=[0.25, 0.0, 0.0], ColorSpace='Diverging',
>> ScalarRangeInitialized=1.0 )
>> a1_Cf_PiecewiseFunction = CreatePiecewiseFunction(
>> Points=[-0.0099065126851201057, 0.0, 0.5, 0.0, 0.029374765232
Re: [Paraview] Help with memory crash?
So I did some more tests by running the script interactively. I used a
smaller grid first, 2002 x 20 x 1000 points and ran it only for 1
iteration. When Paraview loaded the memory usage on the server was 1.04GB.
After doing one iteration the memory usage spiked to 10.42GB and remained
like that when the script finished. What I found out is the Delete
statements make no difference at all, with or without them the memory usage
remained 10.42GB. Performing more iterations in the script actually worsens
this problem, after 4 iterations the memory used increased to 14.32GB. With
a larger grid of 2002 x 100 x 1000 points the memory after one iteration
increased from 10.42GB before the script to 45.25GB after the script. How
can I properly delete all datasets and clear the memory in Paraview?
On Wed, Jan 7, 2015 at 2:55 PM, Nikolaos Beratlis
wrote:
> I am trying to run a script on a cluster with Paraview in parallel. The
> cluster architecture is 16cores and 64GB per node. The script reads in two
> XMF files, one contains a grid of 2002x100x1000 points along with one
> variable. There is a loop to perform two iterations:
>
> try: paraview.simple
> except: from paraview.simple import *
> paraview.simple._DisableFirstRenderCameraReset()
>
> RenderView1 = GetRenderView()
> RenderView1.Background = [1.0, 1.0, 1.0]
> view = GetActiveView()
> view.ViewSize = [ 800, 500 ]
>
> RenderView1.CenterAxesVisibility = 0
> #RenderView1.OrientationAxesVisibility = 0
>
> #Define variables
> wdir =
> '/lustre/groups/balarasgrp/nikosb/Research/Simulations/golfball/stationary/S120/Re20/gridC1/run_wm'
> #wdir =
> '/Users/nikosb/colone/Research/Simulations/golfball/stationary/S120/Re20/gridC1/run_wm'
> #wdir = '/Users/nikosb/Research/Simulations/SPHERE/Re100/gridC1/run'
> Qval = 0.1
> cfmin = -0.001
> cfmax = 0.005
>
> index = [None]*
>
> m = 0
> for i in range(0, 9):
> for j in range(0, 9):
> for k in range(0, 9):
> for l in range(0, 9):
> index[m] = chr(i+48)+chr(j+48)+chr(k+48)+chr(l+48)
> m = m+1
>
>
> for i in range(1,3):
>
> cf_VP_xmf = XDMFReader(
> FileName=wdir+'/VPfield/XDMF/cf_VP'+index[i]+'.xmf' )
>
> cf_VP_xmf.Sets = []
> cf_VP_xmf.Grids = ['STL Grid']
> cf_VP_xmf.PointArrays = ['Cf']
>
> RenderView1 = GetRenderView()
> RenderView1.CenterOfRotation = [6.2286853790283203e-06,
> 2.5033950805664062e-06, 7.1227550506591797e-06]
>
> DataRepresentation1 = Show()
> DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5762951094835]
> DataRepresentation1.SelectionPointFieldDataArrayName = 'Cf'
> DataRepresentation1.ColorArrayName = ('POINT_DATA', 'Cf')
> DataRepresentation1.ScalarOpacityUnitDistance = 0.03392870483226
> DataRepresentation1.ScaleFactor = 0.08557567596444
>
> a1_Cf_PVLookupTable = GetLookupTableForArray( "Cf", 1,
> RGBPoints=[-0.0099065126851201057, 0.23001,
> 0.29899, 0.754, 0.0097341262735426426, 0.86499,
> 0.86499, 0.86499, 0.029374765232205391,
> 0.70596, 0.016, 0.14999], VectorMode='Magnitude',
> NanColor=[0.25, 0.0, 0.0], ColorSpace='Diverging',
> ScalarRangeInitialized=1.0 )
> a1_Cf_PiecewiseFunction = CreatePiecewiseFunction(
> Points=[-0.0099065126851201057, 0.0, 0.5, 0.0, 0.029374765232205391, 1.0,
> 0.5, 0.0] )
>
> DataRepresentation1.ScalarOpacityFunction = a1_Cf_PiecewiseFunction
> DataRepresentation1.LookupTable = a1_Cf_PVLookupTable
>
> a1_Cf_PVLookupTable.ScalarOpacityFunction = a1_Cf_PiecewiseFunction
>
> a1_Cf_PVLookupTable.RGBPoints = [cfmin, 0.23001,
> 0.29899, 0.754, -0.002, 0.86499,
> 0.86499, 0.86499, cfmax, 0.70596,
> 0.016, 0.14999]
> a1_Cf_PVLookupTable.ScalarOpacityFunction = a1_Cf_PiecewiseFunction
> a1_Cf_PVLookupTable.LockScalarRange = 1
>
> RenderView1.CameraPosition = [6.2286853790283203e-06,
> 2.5033950805664062e-06, 3.3460035306026636]
> RenderView1.CameraFocalPoint = [6.2286853790283203e-06,
> 2.5033950805664062e-06, 7.1227550506591797e-06]
> RenderView1.CameraClippingRange = [2.3175641399614015,
> 4.6486514901655163]
> RenderView1.CameraParallelScale = 0.86600759519558368
>
> Contour1 = Contour( PointMergeMethod="Uniform Binning" )
>
> Contour1.PointMergeMethod = "Uniform Binning"
> Contour1.ContourBy = ['POINTS', 'Cf']
> Contour1.Isosurfaces = [0.0097341262735426426]
>
> DataRepresentation2 = Show()
> DataRepresentation2.ColorArrayName = ('P
[Paraview] Help with memory crash?
I am trying to run a script on a cluster with Paraview in parallel. The
cluster architecture is 16cores and 64GB per node. The script reads in two
XMF files, one contains a grid of 2002x100x1000 points along with one
variable. There is a loop to perform two iterations:
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
RenderView1 = GetRenderView()
RenderView1.Background = [1.0, 1.0, 1.0]
view = GetActiveView()
view.ViewSize = [ 800, 500 ]
RenderView1.CenterAxesVisibility = 0
#RenderView1.OrientationAxesVisibility = 0
#Define variables
wdir =
'/lustre/groups/balarasgrp/nikosb/Research/Simulations/golfball/stationary/S120/Re20/gridC1/run_wm'
#wdir =
'/Users/nikosb/colone/Research/Simulations/golfball/stationary/S120/Re20/gridC1/run_wm'
#wdir = '/Users/nikosb/Research/Simulations/SPHERE/Re100/gridC1/run'
Qval = 0.1
cfmin = -0.001
cfmax = 0.005
index = [None]*
m = 0
for i in range(0, 9):
for j in range(0, 9):
for k in range(0, 9):
for l in range(0, 9):
index[m] = chr(i+48)+chr(j+48)+chr(k+48)+chr(l+48)
m = m+1
for i in range(1,3):
cf_VP_xmf = XDMFReader(
FileName=wdir+'/VPfield/XDMF/cf_VP'+index[i]+'.xmf' )
cf_VP_xmf.Sets = []
cf_VP_xmf.Grids = ['STL Grid']
cf_VP_xmf.PointArrays = ['Cf']
RenderView1 = GetRenderView()
RenderView1.CenterOfRotation = [6.2286853790283203e-06,
2.5033950805664062e-06, 7.1227550506591797e-06]
DataRepresentation1 = Show()
DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5762951094835]
DataRepresentation1.SelectionPointFieldDataArrayName = 'Cf'
DataRepresentation1.ColorArrayName = ('POINT_DATA', 'Cf')
DataRepresentation1.ScalarOpacityUnitDistance = 0.03392870483226
DataRepresentation1.ScaleFactor = 0.08557567596444
a1_Cf_PVLookupTable = GetLookupTableForArray( "Cf", 1,
RGBPoints=[-0.0099065126851201057, 0.23001,
0.29899, 0.754, 0.0097341262735426426, 0.86499,
0.86499, 0.86499, 0.029374765232205391,
0.70596, 0.016, 0.14999], VectorMode='Magnitude',
NanColor=[0.25, 0.0, 0.0], ColorSpace='Diverging',
ScalarRangeInitialized=1.0 )
a1_Cf_PiecewiseFunction = CreatePiecewiseFunction(
Points=[-0.0099065126851201057, 0.0, 0.5, 0.0, 0.029374765232205391, 1.0,
0.5, 0.0] )
DataRepresentation1.ScalarOpacityFunction = a1_Cf_PiecewiseFunction
DataRepresentation1.LookupTable = a1_Cf_PVLookupTable
a1_Cf_PVLookupTable.ScalarOpacityFunction = a1_Cf_PiecewiseFunction
a1_Cf_PVLookupTable.RGBPoints = [cfmin, 0.23001,
0.29899, 0.754, -0.002, 0.86499,
0.86499, 0.86499, cfmax, 0.70596,
0.016, 0.14999]
a1_Cf_PVLookupTable.ScalarOpacityFunction = a1_Cf_PiecewiseFunction
a1_Cf_PVLookupTable.LockScalarRange = 1
RenderView1.CameraPosition = [6.2286853790283203e-06,
2.5033950805664062e-06, 3.3460035306026636]
RenderView1.CameraFocalPoint = [6.2286853790283203e-06,
2.5033950805664062e-06, 7.1227550506591797e-06]
RenderView1.CameraClippingRange = [2.3175641399614015, 4.6486514901655163]
RenderView1.CameraParallelScale = 0.86600759519558368
Contour1 = Contour( PointMergeMethod="Uniform Binning" )
Contour1.PointMergeMethod = "Uniform Binning"
Contour1.ContourBy = ['POINTS', 'Cf']
Contour1.Isosurfaces = [0.0097341262735426426]
DataRepresentation2 = Show()
DataRepresentation2.ColorArrayName = ('POINT_DATA', '')
DataRepresentation2.ScaleFactor = 0.099971860647201538
DataRepresentation2.SelectionPointFieldDataArrayName = 'Cf'
DataRepresentation2.EdgeColor = [0.0, 0.0, 0.5762951094835]
DataRepresentation2.Representation = 'Wireframe'
DataRepresentation2.AmbientColor = [0.0, 0.0, 0.0]
DataRepresentation1.Visibility = 0
RenderView1.CameraClippingRange = [2.7470738944403328, 4.2397684828477349]
DataRepresentation1.Visibility = 1
RenderView1.CameraClippingRange = [2.3175641399614015, 4.6486514901655163]
Q_VP_xmf = XDMFReader( FileName=wdir+'/VPfield/XDMF/Q_VP'+index[i]+'.xmf'
)
Contour1.Isosurfaces = [0.0]
Q_VP_xmf.Sets = []
Q_VP_xmf.Grids = ['Eulerian Grid']
Q_VP_xmf.PointArrays = ['Q']
DataRepresentation3 = Show()
DataRepresentation3.EdgeColor = [0.0, 0.0, 0.5762951094835]
DataRepresentation3.SelectionPointFieldDataArrayName = 'Q'
DataRepresentation3.ScalarOpacityUnitDistance = 0.0045778956118952439
DataRepresentation3.Representation = 'Outline'
DataRepresentation3.ScaleFactor = 0.25585924386978148
RenderView1.CameraClippingRange = [0.30866115510384229,
6.131182592065]
Contour2 = Contour( PointMergeMethod="Uniform Binning" )
Contour2.PointMergeMethod = "Uniform Binning"
Contour2.ContourBy = ['POINTS', 'Q']
Contour2.Isosurfaces = [-348374.28125]
DataRepresentation4 = Show()
DataRepresentation4.ScaleFactor = 0.1348903000354767
DataRepresentation4.SelectionPointFieldDataArrayName = 'Normals'
DataRepres
[Paraview] Help with reading vectors from XDMF
I want to read a XDMF file with an orthogonal structured grid and a vector attribute. I have the following example file: http://www.w3.org/2003/XInclude"; Version="2.2"> 0.0 1.0 0.0 1.0 0.0 1.0 -1.0 1.0 -1.0 1.0 -1.0 1.0 -1.0 0.0 0.0 0.0 0.0 However Paraview reads it wrong, the values of the velocity in the information window range from -1e+299 to 1e299. Where is the mistake that causes Paraview to read the wrong values? Thank you, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Help with reading vectors from XDMF
When I read the following file: http://www.w3.org/2003/XInclude"; Version="2.2"> 0.0 1.0 0.0 1.0 0.0 1.0 -1.0 1.0 -1.0 1.0 -1.0 1.0 -1.0 0.0 0.0 0.0 0.0 Paraview reads it wrong, the values of the velocity in the information window range from -1e+299 to 1e299. Where is the mistake that causes Paraview to read the wrong values? Thank you, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Help with reading vectors from XDMF
I have following XDMF file: http://www.w3.org/2003/XInclude"; Version="2.2"> 0.0 1.0 0.0 1.0 0.0 1.0 -1.0 1.0 -1.0 1.0 -1.0 1.0 -1.0 0.0 0.0 0.0 I can read it into Paraview but when I try to plot vectors using the Glyph Filter the vectors are not correct (see attached picture). What am I doing wrong? Kind regards, Nikos <>___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Paraview in batch and in parallel
I read in Paraview Wiki that as of Paraview 3.10 the MPI library is packaged in the binary release. Do I still need to have an MPI version installed on my computer to run Paraview in parallel in batch mode (pvbatch)? If MPI is not required, then how do I run pvbatch in parallel. Is there an argument to specify to use multi core on shared memory clusters? Otherwise I assume that a MPI version is required and I'd run it using "mpiexec -n Nprocs pvbatch python.py" Thank you, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Memory leak with Python script (XDMF and HDF5)
I am using the following python script to extract images from a series of
files for an animation:
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
index = [None]*
m = 0
for i in range(0, 9):
for j in range(0, 9):
for k in range(0, 9):
for l in range(0, 9):
index[m] = chr(i+48)+chr(j+48)+chr(k+48)+chr(l+48)
m = m+1
for i in range(1,2):
cf_VP_anim_xmf = XDMFReader( FileName='XDMF/cf_VP'+index[i]+'.xmf' )
cf_VP_anim_xmf.CellArrays = []
cf_VP_anim_xmf.Sets = []
cf_VP_anim_xmf.PointArrays = ['Cf']
RenderView1 = GetRenderView()
a1_Cf_PVLookupTable = GetLookupTableForArray( "Cf", 1 )
Cfcontours = Show()
Cfcontours.EdgeColor = [0.0, 0.0, 0.5762951094835]
Cfcontours.SelectionPointFieldDataArrayName = 'Cf'
Cfcontours.ScalarOpacityFunction = []
Cfcontours.ColorArrayName = 'Cf'
Cfcontours.ScalarOpacityUnitDistance = 2.4071425938556859
Cfcontours.LookupTable = a1_Cf_PVLookupTable
Cfcontours.ScaleFactor = 15.0
cf_VP_anim_xmf.Grids = ['STL Grid']
RenderView1.CacheKey = 2.0
RenderView1.CameraClippingRange = [288.47079837284241,
299.16435388730815]
RenderView1.UseCache = 0
a1_Cf_PVLookupTable.RGBPoints = [-0.0080002, 0.0, 0.0, 1.0,
0.0080002, 1.0, 0.0, 0.0]
a1_Cf_PVLookupTable.LockScalarRange = 1
separationline = Contour( PointMergeMethod="Uniform Binning" )
separationline.ContourBy = ['POINTS', 'Cf']
separationline.Isosurfaces = [0.0]
DataSeparationLine = Show()
DataSeparationLine.ScaleFactor = 12.321390008926393
DataSeparationLine.SelectionPointFieldDataArrayName = 'Cf'
DataSeparationLine.EdgeColor = [0.0, 0.0, 0.5762951094835]
DataSeparationLine.LineWidth = 2.0
DataSeparationLine.DiffuseColor = [0.0, 0.0, 0.0]
DataSeparationLine.ColorArrayName = ''
Cfcontours.Visibility = 1
Q_VP_xmf = XDMFReader( FileName='XDMF/Q_VP'+index[i]+'.xmf' )
Q_VP_xmf.CellArrays = []
Q_VP_xmf.Sets = []
Q_VP_xmf.PointArrays = ['Q']
DataQ = Show()
DataQ.Representation = 'Outline'
DataQ.ScaleFactor = 12.341455459594727
DataQ.SelectionPointFieldDataArrayName = 'Q'
DataQ.EdgeColor = [0.0, 0.0, 0.5762951094835]
Q_VP_xmf.Grids = ['Eulerian Grid']
ContourQ = Contour( PointMergeMethod="Uniform Binning" )
ContourQ.PointMergeMethod = "Uniform Binning"
ContourQ.ContourBy = ['POINTS', 'Q']
ContourQ.Isosurfaces = [1.0]
ContourQ.ComputeNormals = 0
DataQiso = Show()
DataQiso.ScaleFactor = 7.497686161037
DataQiso.SelectionPointFieldDataArrayName = 'Normals'
DataQiso.EdgeColor = [0.0, 0.0, 0.5762951094835]
DataQ.Visibility = 0
#--- Setup view
RenderView1 = GetRenderView()
RenderView1.Background = [1.0, 1.0, 1.0]
RenderView1.CenterAxesVisibility = 0
RenderView1.OrientationAxesVisibility = 0
RenderView1.ViewSize = [2000, 350]
RenderView1.CameraViewUp = [0.0,-1.0, -2.2204460492503131e-16]
RenderView1.CameraPosition = [41.5, 0.0, 56.5]
RenderView1.CameraClippingRange = [120.40716073726786,
126.85668499830999]
RenderView1.InteractionMode = '3D'
RenderView1.CameraFocalPoint = [0, 0, 56.5]
RenderView1.CenterOfRotation = [0, 0, 56.5]
#--- Export image
Render()
WriteImage('Q_cf_topview_'+index[i]+'.jpg')
#--- Delete objects (order is important)
Delete(DataSeparationLine)
Delete(separationline)
Delete(Cfcontours)
Delete(cf_VP_anim_xmf)
Delete(DataQiso)
Delete(ContourQ)
Delete(DataQ)
Delete(Q_VP_xmf)
At the end of the for loop, I delete all the objects and readers. I run
this python script in batch mode (Paraview 3.98) and in parallel with 4
processors. However I am having a memory leak, by the 6th time in the for
loop it complains about insufficient memory. Can anyone understand what is
causing the memory to increase? Do I forget to delete sth?
Thank you,
Nikos
___
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Please keep messages on-topic and check the ParaView Wiki at:
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Follow this link to subscribe/unsubscribe:
http://www.paraview.org/mailman/listinfo/paraview
[Paraview] XY plot in Paraview
I am reading a structured orthogonal grid and a variable with the following XDMF file: ../VPfield_files/grid3dc_VP.h5sp:/X ../VPfield_files/grid3dc_VP.h5sp:/Y ../VPfield_files/grid3dc_VP.h5sp:/Z ../Tuu_tmavg.h5sp:/var3d How can I make a XY plot of the scalar variable passing through a line or by limiting the indices of the variables (i.e. i=1-NX, j=3, k=4) ? Is there a command similar to slice but for a line? Thank you, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Help with batch processing and loops
Hi, I am switching to using Paraview from Tecplot and I need to do the following thing: I have a series of XDMF files that I need to read into Paraview one by one, apply some filters and export an image. In Tecplot I would write a macro, inside the macro there was a loop that changed the name of the file, then read the filename and in a style that applied all the filters and finally exported an image. I would run the macro in batch mode. How can I do sth similar in Paraview? I have no experience with python. Kind regards, Nikos ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Attribute for grid collection
When I try to transform the "Collection" grid from cartesian coordinates to cylindrical coordinates using the following script: pdi = self.GetInput() pdo = self.GetOutput() newPoints = vtk.vtkPoints() numPoints = pdi.GetNumberOfPoints() for i in range(0, numPoints): coord = pdi.GetPoint(i) x, y, z = coord[:3] r = x * cos(y) t = x * sin(y) newPoints.InsertPoint(i, r, t, z) pdo.SetPoints(newPoints) pdo.GetPointData().AddArray(pdi.GetPointData().GetArray(0)) pdo.GetPointData().AddArray(pdi.GetPointData().GetArray(1)) pdo.GetPointData().AddArray(pdi.GetPointData().GetArray(2)) I get the following error: Traceback (most recent call last): File "", line 26, in File "", line 7, in RequestData AttributeError: GetPoint The script works well if the grid is not of GridType Collection. Thank you, Nikos On Thu, Apr 4, 2013 at 3:57 AM, Felipe Bordeu wrote: > you must put the attributes inside each grid: > > Felipe > > > > > > > > > > > Format="XML"> >0. 1. 2. > > Format="XML"> >0. 2.0944 4.1888 6.2832 > > Format="XML"> >1. 2. > > > > Format="XML"> > >0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 > > > > > > > > >1. 2. 3. > > > 0. 2.0944 4.1888 6.2832 > > >2. 3. > > > > Format="XML"> > > 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 > > > > > > > > > Le 04/04/2013 04:36, Nikolaos Beratlis a écrit : > > I have a domain that consists of patches of orthogonal cartesian grids in > the following XDMF file: > > > > > > > > > > >0. 1. 2. > > >0. 2.0944 4.1888 6.2832 > > >1. 2. > > > > > > > >1. 2. 3. > > >0. 2.0944 4.1888 6.2832 > > >2. 3. > > > > > > 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 > 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 > > > > > > > The grid is declared as GridType Collection. When I read it in Paraview > the grid is read correctly as shown in the attached picture, however I > don't get the values for the attribute. I think the attribute is not read > at all. Is there sth wrong with this file? How should the attribute be > specified for GridType Collection? > > Thank you, > > Nikos > > > ___ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the ParaView Wiki at: > http://paraview.org/Wiki/ParaView > > Follow this link to > subscribe/unsubscribe:http://www.paraview.org/mailman/listinfo/paraview > > > > -- > Felipe Bordeu Weldt > Ingénieur de Recherche > - > Tél. : 33 (0)2 40 37 16 57 > Fax. : 33 (0)2 40 74 74 06felipe.bor...@ec-nantes.fr > Institut GeM - UMR CNRS 6183 > École Centrale Nantes > 1 Rue de La Noë, 44321 Nantes, FRANCE > - > > > ___ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the ParaView Wiki at: > http://paraview.org/Wiki/ParaView > > Follow this link to subscribe/unsubscribe: > http://www.paraview.org/mailman/listinfo/paraview > > ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Python scripting/Grid geometry transformation
Hi, I am reading the following xmf file (attached as var3d.xmf) into Paraview: 0. 1. 2. 0. 2.0944 4.1888 6.2832 1. 2. 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 The grid is a 3D orthogonal grid read in cartesian coordinates (see attached image showing grid and contours of variable). I then want to transform the grid from cartesian to cylindrical coordinates. I tried using the following Python script: pdi = self.GetPolyDataInput() pdo = self.GetPolyDataOutput() newPoints = vtk.vtkPoints() numPoints = pdi.GetNumberOfPoints() for i in range(0, numPoints): coord = pdi.GetPoint(i) x, y, z = coord[:3] r = x * sin(y) t = x * cos(y) newPoints.InsertPoint(i, r, t, z) pdo.SetPoints(newPoints) with Output Data Set Type chosen to be the Same as Input, but I get this error: Traceback (most recent call last): File "", line 26, in File "", line 12, in RequestData AttributeError: 'NoneType' object has no attribute 'SetPoints' I have no experience with Python scripting. What am I doing wrong? Thank you, Nikos <> var3d.xmf Description: Binary data ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] XDMF and structured grid in cylindrical coordinates (curvilinear)
I am currently trying the Function itemtype approach. In all of the examples for the function itemtype it is assumed that arrays are all of the same size. In my case I have three 1D arrays of different sizes: x(nx), y(ny), and z(nz). The operation I need to do to convert to cylindrical coordinates is: do k=1,nz do j=1,ny do i=1,nx x(i)*sin(y(j)), x(i)*cos(y(j)), z(k) enddo enddo enddo I know that function has the operations SIN and COS but can the nested looping be achieved with a function operation? Thank you, Nikos On Wed, Mar 20, 2013 at 10:57 AM, David E DeMarle wrote: > See if XDMF's Function itemtype will do the trick. (If so please consider > posting an example to the xdmf.org wiki). > > Otherwise you'll have to apply a filter to do the geometry transformation > after you load the RectMesh into ParaView. > > > David E DeMarle > Kitware, Inc. > R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4909 > > > On Wed, Mar 20, 2013 at 10:52 AM, Nikolaos Beratlis < > nikos.berat...@gmail.com> wrote: > >> Hi David, >> >> I looked at your examples and I noticed that you changed the GeometryType >> to XYZ in order to plot a curvilinear grid. So it can't be done by >> specifying three separate 1D arrays instead (GeometryType=VXVYVZ)? My only >> concern is storage as I use grids with sizes of 2000x2000x2000. Writing >> that to a file will be huge compared to writing only three 1D arrays as I >> do for the cartesian case. Or is there a way to convert a grid read in >> cartesian coordinates to cylindrical the way it's done in Tecplot? >> >> Thank you. >> >> Nikos >> >> >> On Wed, Mar 20, 2013 at 10:18 AM, David E DeMarle < >> dave.dema...@kitware.com> wrote: >> >>> XDMF's 3DRectMesh == VTK's vtkRectilinearGrid, in which you case you >>> specify an X array, Y array and a Z array. >>> >>> 3DSMesh == vtkStructuredGrid, in which case you specify X,Y,Z for every >>> node. Once you do that you're example will work. >>> >>> Examples of both (produced in ParaView via Data Object Generator (RG1 | >>> SG1)->Write as XDMF) are attached. >>> >>> >>> >>> David E DeMarle >>> Kitware, Inc. >>> R&D Engineer >>> 21 Corporate Drive >>> Clifton Park, NY 12065-8662 >>> Phone: 518-881-4909 >>> >>> >>> On Tue, Mar 19, 2013 at 11:04 PM, Nikolaos Beratlis < >>> nikos.berat...@gmail.com> wrote: >>> >>>> I am using a 3D structured orthogonal grid in cylindrical coordinates. >>>> I can read the grid as a cartesian grid using the following XDMF file by >>>> specifying TopologyType "3DRectMesh" and GeometryType="VXVYVZ" (see >>>> attached image): >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 0.0 1.0 2.0 3.0 4.0 5.0 >>>> >>>> >>>> 0.0 1.5708 3.1415 4.7124 >>>> >>>> >>>> 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 >>>> >>>> >>>> >>>> >>>> >>>> >>>> When I try to read the grid as 3DSMesh which I think corresponds to >>>> curvilinear Paraview crashes. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 0.0 1.0 2.0 3.0 4.0 5.0 >>>> >>>> >>>> 0.0 1.5708 3.1415 4.7124 >>>> >>>> >>>> 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 >>>> >>>> >>>> >>>> >>>> >>>> >>>> Is there any way to read a 3D cylindrical grid using three 1D arrays >>>> for the coordinates in each direction? >>>> >>>> Thank you, >>>> >>>> Nikos >>>> >>>> >>>> >>>> ___ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Please keep messages on-topic and check the ParaView Wiki at: >>>> http://paraview.org/Wiki/ParaView >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://www.paraview.org/mailman/listinfo/paraview >>>> >>>> >>> >> > ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] XDMF and structured grid in cylindrical coordinates (curvilinear)
I am currently trying the Function itemtype approach. In all of the examples for the function itemtype it assumes that arrays are all of the same size. In my case I have three 1D arrays of different sizes: x(nx), y(ny), and z(nz). The operation I need to do to convert to cylindrical coordinates is: do k=1,nz On Wed, Mar 20, 2013 at 10:57 AM, David E DeMarle wrote: > See if XDMF's Function itemtype will do the trick. (If so please consider > posting an example to the xdmf.org wiki). > > Otherwise you'll have to apply a filter to do the geometry transformation > after you load the RectMesh into ParaView. > > > David E DeMarle > Kitware, Inc. > R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4909 > > > On Wed, Mar 20, 2013 at 10:52 AM, Nikolaos Beratlis < > nikos.berat...@gmail.com> wrote: > >> Hi David, >> >> I looked at your examples and I noticed that you changed the GeometryType >> to XYZ in order to plot a curvilinear grid. So it can't be done by >> specifying three separate 1D arrays instead (GeometryType=VXVYVZ)? My only >> concern is storage as I use grids with sizes of 2000x2000x2000. Writing >> that to a file will be huge compared to writing only three 1D arrays as I >> do for the cartesian case. Or is there a way to convert a grid read in >> cartesian coordinates to cylindrical the way it's done in Tecplot? >> >> Thank you. >> >> Nikos >> >> >> On Wed, Mar 20, 2013 at 10:18 AM, David E DeMarle < >> dave.dema...@kitware.com> wrote: >> >>> XDMF's 3DRectMesh == VTK's vtkRectilinearGrid, in which you case you >>> specify an X array, Y array and a Z array. >>> >>> 3DSMesh == vtkStructuredGrid, in which case you specify X,Y,Z for every >>> node. Once you do that you're example will work. >>> >>> Examples of both (produced in ParaView via Data Object Generator (RG1 | >>> SG1)->Write as XDMF) are attached. >>> >>> >>> >>> David E DeMarle >>> Kitware, Inc. >>> R&D Engineer >>> 21 Corporate Drive >>> Clifton Park, NY 12065-8662 >>> Phone: 518-881-4909 >>> >>> >>> On Tue, Mar 19, 2013 at 11:04 PM, Nikolaos Beratlis < >>> nikos.berat...@gmail.com> wrote: >>> >>>> I am using a 3D structured orthogonal grid in cylindrical coordinates. >>>> I can read the grid as a cartesian grid using the following XDMF file by >>>> specifying TopologyType "3DRectMesh" and GeometryType="VXVYVZ" (see >>>> attached image): >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 0.0 1.0 2.0 3.0 4.0 5.0 >>>> >>>> >>>> 0.0 1.5708 3.1415 4.7124 >>>> >>>> >>>> 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 >>>> >>>> >>>> >>>> >>>> >>>> >>>> When I try to read the grid as 3DSMesh which I think corresponds to >>>> curvilinear Paraview crashes. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 0.0 1.0 2.0 3.0 4.0 5.0 >>>> >>>> >>>> 0.0 1.5708 3.1415 4.7124 >>>> >>>> >>>> 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 >>>> >>>> >>>> >>>> >>>> >>>> >>>> Is there any way to read a 3D cylindrical grid using three 1D arrays >>>> for the coordinates in each direction? >>>> >>>> Thank you, >>>> >>>> Nikos >>>> >>>> >>>> >>>> ___ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Please keep messages on-topic and check the ParaView Wiki at: >>>> http://paraview.org/Wiki/ParaView >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://www.paraview.org/mailman/listinfo/paraview >>>> >>>> >>> >> > ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] XDMF and structured grid in cylindrical coordinates (curvilinear)
Hi David, I looked at your examples and I noticed that you changed the GeometryType to XYZ in order to plot a curvilinear grid. So it can't be done by specifying three separate 1D arrays instead (GeometryType=VXVYVZ)? My only concern is storage as I use grids with sizes of 2000x2000x2000. Writing that to a file will be huge compared to writing only three 1D arrays as I do for the cartesian case. Or is there a way to convert a grid read in cartesian coordinates to cylindrical the way it's done in Tecplot? Thank you. Nikos On Wed, Mar 20, 2013 at 10:18 AM, David E DeMarle wrote: > XDMF's 3DRectMesh == VTK's vtkRectilinearGrid, in which you case you > specify an X array, Y array and a Z array. > > 3DSMesh == vtkStructuredGrid, in which case you specify X,Y,Z for every > node. Once you do that you're example will work. > > Examples of both (produced in ParaView via Data Object Generator (RG1 | > SG1)->Write as XDMF) are attached. > > > > David E DeMarle > Kitware, Inc. > R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4909 > > > On Tue, Mar 19, 2013 at 11:04 PM, Nikolaos Beratlis < > nikos.berat...@gmail.com> wrote: > >> I am using a 3D structured orthogonal grid in cylindrical coordinates. I >> can read the grid as a cartesian grid using the following XDMF file by >> specifying TopologyType "3DRectMesh" and GeometryType="VXVYVZ" (see >> attached image): >> >> >> >> >> >> >> >> >> >> 0.0 1.0 2.0 3.0 4.0 5.0 >> >> >> 0.0 1.5708 3.1415 4.7124 >> >> >> 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 >> >> >> >> >> >> >> When I try to read the grid as 3DSMesh which I think corresponds to >> curvilinear Paraview crashes. >> >> >> >> >> >> >> >> >> >> 0.0 1.0 2.0 3.0 4.0 5.0 >> >> >> 0.0 1.5708 3.1415 4.7124 >> >> >> 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 >> >> >> >> >> >> >> Is there any way to read a 3D cylindrical grid using three 1D arrays for >> the coordinates in each direction? >> >> Thank you, >> >> Nikos >> >> >> >> ___ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Please keep messages on-topic and check the ParaView Wiki at: >> http://paraview.org/Wiki/ParaView >> >> Follow this link to subscribe/unsubscribe: >> http://www.paraview.org/mailman/listinfo/paraview >> >> > ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] XDMF and structured grid in cylindrical coordinates (curvilinear)
I am using a 3D structured orthogonal grid in cylindrical coordinates. I can read the grid as a cartesian grid using the following XDMF file by specifying TopologyType "3DRectMesh" and GeometryType="VXVYVZ" (see attached image): 0.0 1.0 2.0 3.0 4.0 5.0 0.0 1.5708 3.1415 4.7124 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 When I try to read the grid as 3DSMesh which I think corresponds to curvilinear Paraview crashes. 0.0 1.0 2.0 3.0 4.0 5.0 0.0 1.5708 3.1415 4.7124 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 Is there any way to read a 3D cylindrical grid using three 1D arrays for the coordinates in each direction? Thank you, Nikos <>___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Reading PLOT3D into Paraview
Hi, I have problems reading PLOT3D files into paraview. Here is a small test file containing the grid: 1 3 2 2 0.0 1.0 2.0 0.0 1.0 2.0 0.0 1.0 2.0 0.0 1.0 2.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 The grid is a 3D one, it has one block with size 3x2x2 and the format is ASCII. I can read this file into Tecplot without any problem but when I try to read it into Paraview 3.98 I get the following error: ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-NoMPI/paraview/src/paraview/ParaViewCore/VTKExtensions/Default/vtkFileSeriesReader.cxx, line 690 vtkFileSeriesReader (0x11713e850): Inputs are not set. What is wrong, the file itself or the PLOT3D reader of Paraview? Thank you, Nikos <>___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
