Hi everyone, I am in the field of atomic simulation. Paraview can display atoms beautifully, but I currently cannot find a way to draw bonds between atoms within certain distance. Can anyone help me with this? Thanks very much.
Best Regards, LJ On Thu, Oct 3, 2013 at 11:09 AM, <paraview-requ...@paraview.org> wrote: > Send ParaView mailing list submissions to > paraview@paraview.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.paraview.org/mailman/listinfo/paraview > or, via email, send a message with subject or body 'help' to > paraview-requ...@paraview.org > > You can reach the person managing the list at > paraview-ow...@paraview.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of ParaView digest..." > > > Today's Topics: > > 1. Re: My own filter as part of pipeline for coprocessing raises > "name not defined" error (Andy Bauer) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Oct 2013 11:09:15 -0400 > From: Andy Bauer <andy.ba...@kitware.com> > Subject: Re: [Paraview] My own filter as part of pipeline for > coprocessing raises "name not defined" error > To: Hong Yi <hon...@renci.org> > Cc: "paraview@paraview.org" <paraview@paraview.org> > Message-ID: > < > camaop+f1nzkjfhzz9fvnojmsiofbqcsitcqqxbc7ygm8szk...@mail.gmail.com> > Content-Type: text/plain; charset="windows-1252" > > Hmm, I would check the link line for your adaptor and for creating the > executable to see if the plugin library is included there. Something else > you can try is explicitly create the plugin's filter in the adaptor code to > make sure that it is linked in properly. > > Regards, > Andy > > > On Thu, Oct 3, 2013 at 10:41 AM, Hong Yi <hon...@renci.org> wrote: > > > Hi Andy,**** > > > > ** ** > > > > That is exactly what I did, and I also modified CMakeLists.txt to link > > ${PARAVIEW_PLUGINLIST} to the target via target_link_libraries. However, > > the symbol ?pv_plugin_instance_SMVorticity? is undefined in the built > > target static library, while following the same process to build pvbatch > > and pvpython executable works, i.e., the same plugin symbol is defined in > > built pvpython executable. Since it is static linking, I know linking > order > > matters, but have not got it to work by adjusting linking orders. Let me > > know if you have ideas on what I could try to figure out and resolve this > > issue.**** > > > > ** ** > > > > Thanks,**** > > > > ** ** > > > > Hong**** > > > > ** ** > > > > ** ** > > > > *From:* Andy Bauer [mailto:andy.ba...@kitware.com] > > *Sent:* Thursday, October 03, 2013 10:19 AM > > > > *To:* Hong Yi > > *Cc:* David E DeMarle; paraview@paraview.org > > *Subject:* Re: [Paraview] My own filter as part of pipeline for > > coprocessing raises "name not defined" error**** > > > > ** ** > > > > Hi Hong,**** > > > > There won't be a separate library created for Python wrapping your plugin > > for doing ParaView. Did you add in the following to your adaptor:**** > > > > #ifndef BUILD_SHARED_LIBS**** > > > > #include "pvStaticPluginsInit.h"**** > > > > #endif**** > > > > > > And then in the adaptor initialization step you should have something in > > it like:**** > > > > #ifndef BUILD_SHARED_LIBS**** > > > > paraview_static_plugins_init();**** > > > > #endif**** > > > > If that doesn't work then it will probably take a bit of tinkering to > > figure out what's wrong. > > > > Regards, > > Andy**** > > > > ** ** > > > > On Wed, Oct 2, 2013 at 12:28 PM, Hong Yi <hon...@renci.org> wrote:**** > > > > Thanks for the helpful info, Andy. I looked at the link and followed the > > code change Burlen posted to add the static linked plugin initialization > > into pvbatch and pvpython and that worked fine. Now pvbatch and pypthon > all > > have my filter plugin statically loaded. I still got the ?name not > defined? > > error when coprocessing parses the pipeline though. I believe the problem > > remains because there is still no python wrapped proxy to my filter since > > there is no change to lib\site-packages after I add the static linked > > plugin initialization into pybatch and pvpython. To make sure I am on the > > right track for my further investigation, I am hoping to get answers to a > > couple of my further questions below:**** > > > > **** > > > > 1. What is the right way to go to have the proxy to my filter > > Python wrapped? How can I verity I have the proxy to my filter Python > > wrapped? Is it true that the Python-wrapped proxy to my filter should > show > > up in some python file in lib\site-packages if the filter is indeed > > python-wrapped? **** > > > > 2. I made similar changes to CPythonAdaptorAPI.cxx and > > CMakeLists.txt as I did to pvpthon and pvbatch to load and init static > > plugin in function coprocessorinitializewithpython() hoping to have > plugin > > loaded when doing coprocessing linked to simulation, however, I still > have > > the symbol ?pv_plugin_instance_SMVorticity? undefined in built > > PythonCatalyst static lib while the plugin symbol is indeed defined in > > pvpython with the same code changes. Just to confirm, does the plugin > need > > to be loaded in Catalyst initialization in order to use it in a > > coprocessing pipeline? In other words, to get my plugin working in > catalyst > > linked to simulation, I need to resolve two problems: (1) get the plugin > > statically loaded in Catalyst initialization; (2) get the proxy to the > > plugin Python wrapped and show up in some python file in > lib\site-packages. > > Is this true?**** > > > > **** > > > > Yes, I know the gradient of unstructured data set filter can compute > > vorticity, which I referenced to write this custom vorticity filter to > make > > it fit our needs better with better performance. I did try to use the > > genetic gradient filter to compute vorticity for coprocessing, but it > > raises a segmentation fault after outputting several images. Will have to > > debug and investigate more to find out more on that.**** > > > > **** > > > > Thanks,**** > > > > Hong**** > > > > **** > > > > *From:* Andy Bauer [mailto:andy.ba...@kitware.com] > > *Sent:* Tuesday, October 01, 2013 2:19 PM**** > > > > > > *To:* Hong Yi > > *Cc:* David E DeMarle; paraview@paraview.org > > *Subject:* Re: [Paraview] My own filter as part of pipeline for > > coprocessing raises "name not defined" error**** > > > > **** > > > > Hi Hong,**** > > > > I don't think you want to do VTK Python wrapping of your class. What you > > want is to have the proxy to the filter Python wrapped such that it's > > available when you import paraview.simple. This is what's needed for > > Catalyst Python pipelines. I don't think you're properly initializing the > > plugins from the previous directions I sent. You may want to look at > > > http://public.kitware.com/pipermail/paraview-developers/2013-September/002499.html > > **** > > > > As a side note, the gradient of unstructured data set filter can compute > > vorticity as well. It does require a vtkDataArray with three components > to > > use though. **** > > > > Regards, > > Andy**** > > > > **** > > > > On Mon, Sep 30, 2013 at 5:06 PM, Hong Yi <hon...@renci.org> wrote:**** > > > > Thanks, Andy. The CMakeLists.txt for my plugin is copied below with newly > > added lines for python wrapping in orange: > > > > ----------------------------- > > if(NOT ParaView_SOURCE_DIR) > > find_package(ParaView) > > include("${PARAVIEW_USE_FILE}") > > include (ParaViewPlugins) > > else() > > # we're building from within ParaView Source. > > endif() > > > > include_directories(${VTK_INCLUDE_DIRS}) > > include(wrap-python.cmake) > > > > # create a paraview plugin containing server manager xml and the server > > # manager classes to build > > # this plugin can be loaded on the server side > > > > ADD_PARAVIEW_PLUGIN(SMVorticity "1.0" > > SERVER_MANAGER_XML VorticityFilter.xml > > SERVER_MANAGER_SOURCES VorticityFilter.cxx) > > > > target_link_libraries(SMVorticity ${deps}) > > > > if(VTK_WRAP_PYTHON) > > wrap_python(SMVorticity "${sources}") > > endif() > > ----------------------------- > > > > The orange lines are added by following > > http://www.paraview.org/pipermail/paraview/2012-May/024855.html which > > works well and builds my filter and also wraps it in Python (i.e., it > > generates libSMVorticity.a and libSMVorticityPythonD.a). I have also > > verified the plugin is indeed loaded into pvserver and pvpython in > paraview > > built bin directory. > > > > However, I still got "name not defined" error in coprocessing script when > > creating this filter by name "VorticityOfUnstructuredDataSet" in python > > script. I have a couple of specific questions I am currently > investigating > > and hoping to get some inputs from experts in the list: > > > > 1. I am not sure where this name "VorticityOfUnstructuredDataSet" > > (exported by coprocessing script generator plugin) comes from, the only > > clue I can see is in plugin.cmake, where the plugin is specified with > > DESCRIPTION "Vorticity Of Unstructured DataSet" and in > VorticityFilter.xml, > > where the plugin is given a label of "Vorticity Of Unstructured DataSet." > > Should this name be defined somewhere such as in some python file in > > paraview python site-packages? > > > > 2. I did try to add PV_PLUGIN_IMPORT macros to the adaptor since I am > > using Catalyst, however, the plugin symbol > "pv_plugin_instance_SMVorticity" > > is undefined in the adaptor static lib (the same plugin symbol is defined > > in pvserver), hence I got an undefined error when linking simulation code > > to the adaptor. I did try to add my plugin static lib (in which the > plugin > > symbol is defined) to the adaptor target via target_link_libraries before > > linking to vtkPVPythonCatalyst, but that does not seem to take any > effect. > > For some reason I am still investigating, my plugin lib does not get to > > link to the adaptor via target_link_libraries. What I did is to go to src > > directory in the cross target and modified CMakeLists.txt for > > PhastaAdaptor, then went to corresponding paraview-build directory, and > did > > "make clean" followed by "make" to rebuild PhastaAdaptor lib. Is there > > something obvious that I did not do correctly? > > > > Thanks for any inputs! > > > > Hong**** > > ------------------------------ > > > > *From:* Andy Bauer [andy.ba...@kitware.com] > > *Sent:* Friday, September 27, 2013 3:00 PM > > *To:* Hong Yi > > *Cc:* David E DeMarle; paraview@paraview.org**** > > > > > > *Subject:* Re: [Paraview] My own filter as part of pipeline for > > coprocessing raises "name not defined" error**** > > > > **** > > > > Can you share your plugin or at least the CMakeLists.txt for your plugin? > > Have you tried with any other plugins that get packaged with ParaView to > > see if they work?**** > > > > If you're using Catalyst, I would suggest adding in the > > PV_PLUGIN_IMPORT_INIT macros to the adaptor.**** > > > > Andy**** > > > > **** > > > > On Thu, Sep 26, 2013 at 3:40 PM, Hong Yi <hon...@renci.org> wrote:**** > > > > Thanks! I did put my plugin inside ParaView/Plugins in the same way as > > other Plugins, and enabled it when building ParaView superbuild on > Titan. I > > can see the static lib for the Plugin is built in paraview-build/lib > > directory. And yes, I did use a plugin and load it via Tools|Manage > Plugins > > when creating python coprocessing script. However, it looks like my > plugin > > is not loaded automatically even though it is built by ParaView > superbuild. > > Perhaps I should still follow the link > > > http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Plugins_in_Static_Applicationsbut > > I am having some difficulty in following the info in the link to do what > is > > suggested. Specifically, to what file should I insert two macros? It does > > not sound right to insert them into my custom plugin cxx file. Where > should > > I add two macros to get my custom filter plugin to be loaded and wrapper > > into python module? I see "LoadPlugin" function defined in simple.py to > > call servermanager.LoadPlugin(filename, remote) which I am thinking > perhaps > > should be called to load my plugin before my python coprocessing script > is > > executed, but not sure whether this is the case or not. **** > > > > **** > > > > Thanks for any suggestions! **** > > > > **** > > > > Hong**** > > > > **** > > > > **** > > > > *From:* David E DeMarle [mailto:dave.dema...@kitware.com] > > *Sent:* Thursday, September 26, 2013 1:28 PM > > *To:* Andy Bauer > > *Cc:* Hong Yi; paraview@paraview.org > > *Subject:* Re: [Paraview] My own filter as part of pipeline for > > coprocessing raises "name not defined" error**** > > > > **** > > > > Utkarsh pointed out that you still need to follow > > > http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Plugins_in_Static_Applications > > **** > > > > when the plugin is external to ParaView. If you put your plugin inside > > ParaView/Plugins, then it is done automatically.**** > > > > > > **** > > > > David E DeMarle > > Kitware, Inc. > > R&D Engineer > > 21 Corporate Drive > > Clifton Park, NY 12065-8662 > > Phone: 518-881-4909**** > > > > **** > > > > On Thu, Sep 26, 2013 at 12:23 PM, David E DeMarle < > > dave.dema...@kitware.com> wrote:**** > > > > I think that information is out of date. I believe that is done > > automatically now.**** > > > > **** > > > > Otherwise Andy is right. Putting the filter inside a plugin a good way to > > go. The plugin infrastructure will make it so that when you provide the > XML > > that describes your vtk class, ParaView's build system will automatically > > wrap it into a proxy and python class so that ParaView will be able to > use > > it.**** > > > > **** > > > > Also, I recommend trying it on a local static build first. That way the > > build time will be less and development will be quicker. Once you can > load > > you plugin locally, then you should only have to compile on titan > once.*** > > * > > > > **** > > > > > > **** > > > > David E DeMarle > > Kitware, Inc. > > R&D Engineer > > 21 Corporate Drive > > Clifton Park, NY 12065-8662 > > Phone: 518-881-4909**** > > > > **** > > > > On Wed, Sep 25, 2013 at 10:34 PM, Andy Bauer <andy.ba...@kitware.com> > > wrote:**** > > > > Did you use a plugin to add in your custom filter when creating the > Python > > co-processing script? I'm not sure how plugins are "loaded" for static > > builds but you may want to look at > > > http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Plugins_in_Static_Applications > . > > If that doesn't work, we'll have to figure out some other way to do > it.*** > > * > > > > Andy**** > > > > **** > > > > **** > > > > **** > > > > **** > > > > On Wed, Sep 25, 2013 at 9:16 PM, Hong Yi <hon...@renci.org> wrote:**** > > > > Hello, > > > > I set up a pipeline that used a custom filter I developed and exported it > > as a python script for coprocessing. I have made sure the static library > > for my custom filter is built and available in paraview-build/lib > > directory, and I have also linked this custom filter static library along > > with Catalyst libs to the simulation code for coprocessing. However, > when I > > run the simulation linked with ParaView coprocessing for in-situ > > visualization, I got "NameError: name 'MyCustomizedFilterName' is not > > defined" error when the line of my customized filter in my python > > coprocessing script is read in for pipeline coprocessing. What should I > do > > to get my custom filter wrapped in python so that it can be recognized > and > > used as part of the python pipeline script for coprocessing? Any advice > and > > suggestions are very much appreciated. > > > > Thanks, > > > > Hong**** > > > > **** > > > > _______________________________________________ > > 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**** > > > > **** > > > > **** > > > > **** > > > > **** > > > > ** ** > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://www.paraview.org/pipermail/paraview/attachments/20131003/9f68cf01/attachment.htm > > > > ------------------------------ > > _______________________________________________ > 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 > > > End of ParaView Digest, Vol 114, Issue 6 > **************************************** >
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