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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi<br>
vtk can be unstructured too;<br>
the issue is that the vtk file converted from your vtu file using VisIt cannot be read directly by MOAB.
<br>
It would make more sense to make a vtu reader in MOAB, or make a h5m writer in VisIt.<br>
Actually, I am working on that (h5m writer) , but it is in a branch now, it is not part of visit yet.<br>
<br>
I am not sure what is the best solution to your problem now. <br>
How do you plan to use the coupler? <br>
<br>
Iulian<br>
<br>
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<div style="direction: ltr;" id="divRpF931620"><font face="Tahoma" size="2" color="#000000"><b>From:</b> Jie Wu [jie.voo@gmail.com]<br>
<b>Sent:</b> Wednesday, June 01, 2016 5:07 PM<br>
<b>To:</b> Grindeanu, Iulian R.<br>
<b>Cc:</b> moab-dev@mcs.anl.gov<br>
<b>Subject:</b> Re: [MOAB-dev] How can I prepare a .h5m file base on my own calculation<br>
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<div class="" style="word-wrap:break-word">Hi Iulian,
<div class=""><br class="">
</div>
<div class="">I will try to convert from .vtu to .vtk by the tools you mentioned.</div>
<div class=""><br class="">
</div>
<div class="">But as I know, .vtk file is usually used for structured mesh, while .vtu for unstructured mesh. I was just wondering if the conversion from .vtu to .vtk make sense?</div>
<div class=""><br class="">
</div>
<div class="">Here is a small vtu file I used to store mesh and solution information. </div>
<div class=""><br class="">
</div>
<div class="">On the nodes, we have displacements and a scaler damage parameter. We also have some other solution variables on the Integration nodes.</div>
<div class=""><br class="">
</div>
<div class="">Thank you so much for your help.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Jie</div>
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<blockquote type="cite" class="">
<div class="">On Jun 1, 2016, at 5:31 PM, Grindeanu, Iulian R. <<a href="mailto:iulian@mcs.anl.gov" class="" target="_blank">iulian@mcs.anl.gov</a>> wrote:</div>
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Hi,<br class="">
You can try paraview to convert from vtu format to vtk;<br class="">
Moab vtk reader is not very robust, in the sense that there are vtk files it cannot read.<br class="">
You can also try VisIt to convert from vtu to vtk<br class="">
<br class="">
Do you have a small vtu file that you can share? I can try to look at it, to see how it goes.<br class="">
What kind of data do you have at nodes?<br class="">
<br class="">
Iulian<br class="">
<br class="">
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<div id="x_divRpF128615" class="" style="direction:ltr"><font class="" face="Tahoma" size="2"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Jie Wu [<a href="mailto:jie.voo@gmail.com" class="" target="_blank">jie.voo@gmail.com</a>]<br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Wednesday, June 01, 2016 2:42 PM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Grindeanu, Iulian R.<br class="">
<b class="">Cc:</b><span class="x_Apple-converted-space"> </span><a href="mailto:moab-dev@mcs.anl.gov" class="" target="_blank">moab-dev@mcs.anl.gov</a><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [MOAB-dev] How can I prepare a .h5m file base on my own calculation<br class="">
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<div class="">Hi Iulian,
<div class=""><br class="">
</div>
<div class="">Thank you very much for your help. The format we use to store mesh and solution information is .vtu file. </div>
<div class=""><br class="">
</div>
<div class="">I tried to run function ./mbconvert. It can successfully transfer from .h5m to .vtk, and vice versa. </div>
<div class=""><br class="">
</div>
<div class="">But I cannot convert either these 2 format to/from .vtu file. </div>
<div class=""><br class="">
</div>
<div class="">An example error message is like following. </div>
<div class=""><br class="">
</div>
<div class="">Is there any solution for this problem? Any suggestion is greatly appreciated!</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Jie</div>
<div class=""><br class="">
</div>
<div class="">
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">dyn-160-39-11-225:tools jiewu$ ./mbconvert in.vtu out.h5m</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
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<span class="">[0]MOAB ERROR: in.vtu: File is not HDF5!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: set_up_read() line 472 in src/io/ReadHDF5.cpp</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: NULL file handle.!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: is_error() line 133 in src/io/ReadHDF5.hpp</span></div>
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<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
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<span class="">[0]MOAB ERROR: ReadNCDF:: problem opening Netcdf/Exodus II file in.vtu!</span></div>
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<span class="">[0]MOAB ERROR: load_file() line 303 in src/io/ReadNCDF.cpp</span></div>
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<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: Trouble opening file in.vtu!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: load_file() line 68 in src/io/ReadNC.cpp</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: Expected Keyword!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: load_file() line 178 in src/io/ReadABAQUS.cpp</span></div>
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<span class="">0x0 hahhahahah</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: This doesn't appear to be a .cub file!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: load_file() line 310 in src/io/Tqdcfr.cpp</span></div>
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<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: Parsing error at line 1: expected one of { $NOD $MeshFormat } got "<?xml"!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: match_token() line 378 in src/io/FileTokenizer.cpp</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: in.vtu: No such file or directory!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: ascii_read_triangles() line 201 in src/io/ReadSTL.cpp</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: in.vtu: not a binary STL file!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: binary_read_triangles() line 312 in src/io/ReadSTL.cpp</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: in.vtu.node: cannot read file!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: open_file() line 59 in src/io/ReadTetGen.cpp</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: in.vtu: Trouble reading vertices!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: read_vertices() line 129 in src/io/ReadTemplate.cpp</span></div>
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<span class="">[0]MOAB ERROR: --------------------- Error Message ------------------------------------</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: Failed to load file after trying all possible readers!</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: serial_load_file() line 635 in src/Core.cpp</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">[0]MOAB ERROR: load_file() line 526 in src/Core.cpp</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">Failed to load "in.vtu".</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">Error code: MB_INDEX_OUT_OF_RANGE (1)</span></div>
<div class="" style="margin:0px; font-size:14px; line-height:normal; font-family:'Andale Mono'; color:rgb(254,253,201); background-color:rgb(0,0,0)">
<span class="">Error message: Failed to load file after trying all possible readers</span></div>
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<div class="">On Jun 1, 2016, at 12:26 PM, Grindeanu, Iulian R. <<a href="mailto:iulian@mcs.anl.gov" class="" target="_blank">iulian@mcs.anl.gov</a>> wrote:</div>
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Hello,<br class="">
Coupler.cpp depends on a moab instance, so even if you do not use h5m format, if you want to use the coupler, your model has to reside inside a moab instance.<span class="x_Apple-converted-space"> </span><br class="">
Do you care about parallelism or not? Then h5m format is required, otherwise it will be hard to employ parallelism<br class="">
<br class="">
there are several converters available, to h5m format, you can do tools/mbconvert -l to see what is available based on your configuration<br class="">
<br class="">
What format do you use?<br class="">
<br class="">
Iulian<br class="">
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<div id="x_divRpF772430" class="" style="direction:ltr"><font class="" face="Tahoma" size="2"><b class="">From:</b><span class="x_Apple-converted-space"> </span><a href="mailto:moab-dev-bounces@mcs.anl.gov" class="" target="_blank">moab-dev-bounces@mcs.anl.gov</a><span class="x_Apple-converted-space"> </span>[<a href="mailto:moab-dev-bounces@mcs.anl.gov" class="" target="_blank">moab-dev-bounces@mcs.anl.gov</a>]
on behalf of Jie Wu [<a href="mailto:jie.voo@gmail.com" class="" target="_blank">jie.voo@gmail.com</a>]<br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Wednesday, June 01, 2016 9:17 AM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span><a href="mailto:moab-dev@mcs.anl.gov" class="" target="_blank">moab-dev@mcs.anl.gov</a><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>[MOAB-dev] How can I prepare a .h5m file base on my own calculation<br class="">
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<div class="">Hi All,
<div class=""><br class="">
</div>
<div class="">In order to transfer variables from a Source mesh to a Target mesh, I am studying the use of function<span class="x_Apple-converted-space"> </span><i class="">mbcoupler_test.cpp</i><span class="x_Apple-converted-space"> </span>these days. </div>
<div class=""><br class="">
</div>
<div class="">The stuff confusing me is the .h5m file. From the MOAB user guide, I know that .h5m is theMOAB’s native file format. </div>
<div class=""><br class="">
</div>
<div class="">But I don’t know how to prepare a .h5m file based on my own calculation results (which usually contains node coordinates, node connectivities, and nodal variables). As a result, I cannot employ a function like<span class="x_Apple-converted-space"> </span><i class="">./mbcoupler_test</i><span class="x_Apple-converted-space"> </span>to
help me to transfer the mesh variables.</div>
<div class=""><br class="">
</div>
<div class="">Any instruction is deeply appreciated!</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Jie</div>
<div class=""><br class="">
</div>
<br class="">
<div class="">
<div class="">
<div class="">Jie Wu, Ph.D. candidate</div>
<div class="">Department of Geotechnical Engineering, Tongji University</div>
<div class="">Visiting student at Civil Engineering & Engineering Mechanics, Columbia University <br class="">
Add: 500 West 120th Street 641 S.W. Mudd New York, NY 10027<br class="">
Ph: +1(917)822-0942</div>
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