[MOAB-dev] How can I prepare a .h5m file base on my own calculation

[Jie Wu]

Hi Iulian,

Thank you very much for your help. The format we use to store mesh and solution information is .vtu file. 

I tried to run function ./mbconvert. It can successfully transfer from .h5m to .vtk, and vice versa. 

But I cannot convert either these 2 format to/from .vtu file. 

An example error message is like following. 

Is there any solution for this problem? Any suggestion is greatly appreciated!

Best,
Jie

dyn-160-39-11-225:tools jiewu$ ./mbconvert in.vtu out.h5m
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: in.vtu: File is not HDF5!
[0]MOAB ERROR: set_up_read() line 472 in src/io/ReadHDF5.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: NULL file handle.!
[0]MOAB ERROR: is_error() line 133 in src/io/ReadHDF5.hpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: ReadNCDF:: problem opening Netcdf/Exodus II file in.vtu!
[0]MOAB ERROR: load_file() line 303 in src/io/ReadNCDF.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: Trouble opening file in.vtu!
[0]MOAB ERROR: load_file() line 68 in src/io/ReadNC.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: Expected Keyword!
[0]MOAB ERROR: load_file() line 178 in src/io/ReadABAQUS.cpp
0x0 hahhahahah
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: This doesn't appear to be a .cub file!
[0]MOAB ERROR: load_file() line 310 in src/io/Tqdcfr.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: Parsing error at line 1: expected one of { $NOD $MeshFormat } got "<?xml"!
[0]MOAB ERROR: match_token() line 378 in src/io/FileTokenizer.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: in.vtu: No such file or directory!
[0]MOAB ERROR: ascii_read_triangles() line 201 in src/io/ReadSTL.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: in.vtu: not a binary STL file!
[0]MOAB ERROR: binary_read_triangles() line 312 in src/io/ReadSTL.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: in.vtu.node: cannot read file!
[0]MOAB ERROR: open_file() line 59 in src/io/ReadTetGen.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: in.vtu: Trouble reading vertices!
[0]MOAB ERROR: read_vertices() line 129 in src/io/ReadTemplate.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: Failed to load file after trying all possible readers!
[0]MOAB ERROR: serial_load_file() line 635 in src/Core.cpp
[0]MOAB ERROR: load_file() line 526 in src/Core.cpp
Failed to load "in.vtu".
Error code: MB_INDEX_OUT_OF_RANGE (1)
Error message: Failed to load file after trying all possible readers



> On Jun 1, 2016, at 12:26 PM, Grindeanu, Iulian R. <iulian at mcs.anl.gov> wrote:
> 
> Hello,
> 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. 
> Do you care about parallelism or not? Then h5m format is required, otherwise it will be hard to employ parallelism
> 
> there are several converters available, to h5m format, you can do tools/mbconvert -l to see what is available based on your configuration
> 
> What format do you use?
> 
> Iulian
> From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf of Jie Wu [jie.voo at gmail.com]
> Sent: Wednesday, June 01, 2016 9:17 AM
> To: moab-dev at mcs.anl.gov
> Subject: [MOAB-dev] How can I prepare a .h5m file base on my own calculation
> 
> Hi All,
> 
> In order to transfer variables from a Source mesh to a Target mesh, I am studying the use of function mbcoupler_test.cpp these days. 
> 
> The stuff confusing me is the .h5m file. From the MOAB user guide, I know that .h5m is theMOAB’s native file format. 
> 
> 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 ./mbcoupler_test to help me to transfer the mesh variables.
> 
> Any instruction is deeply appreciated!
> 
> Best,
> Jie
> 
> 
> Jie Wu, Ph.D. candidate
> Department of Geotechnical Engineering, Tongji University
> Visiting student at Civil Engineering & Engineering Mechanics, Columbia University 
> Add: 500 West 120th Street 641 S.W. Mudd New York, NY  10027
> Ph: +1(917)822-0942

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