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VDF for FLASH Uniform grid data in 3D

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July 9, 2018 - 10:01am
#1
bmanek_663738
VDF for FLASH Uniform grid data in 3D
Hello all, I am currently dealing with 3D simulations uniform grid data with FLASH code. I came across flashvdfcreate and flashamr2vdf commands for creating VDF files for FLASH HDF5 files. These commands don't seem to be working (probably because they support only AMR data?). Can someone please guide me to a reference to sort out this issue or suggest any ideas regarding this? Thanks, Bhishek.
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July 9, 2018 - 1:22pm
clyne

Hi Bhishek,

 

The flash* commands do indeed expect AMR data. If you have regular strucutred data from FLASH your best be is to output/convert the data to "raw" binaries and then use the combination of vdfcreate and raw2vdf, or possibly convert your data to NetCDF format and use ncdfvdfcreate/ncdf2vdf as described here: https://www.vapor.ucar.edu/docs/usage/vapor-data-preparation

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November 27, 2018 - 8:33pm
bmanek_663738
Hello, Thank you for the answer. I was able to successfully use the vdfcreate and raw2vdf commands by converting the hdf5 files to raw binaries. The issue I am facing now is that the orientation of the axes and variable is not proper. I tried to specify the -extent in vdfcreate and also the -dimension options but it doesn't work. My data is in x=[-1,1], y=[0,4], z=[-2,2] with nx=200, ny=400, nz=400. I use the following commands - 1. h5dump -d /magz -b LE -o BINARY_FILE HDF5_FILE 2. vdfcreate -dimension 200x400x800 -varnames magz VDF_FILE 3. raw2vdf VDF_FILE BINARY_FILE. The magz variable should be aligned along the z-axis but on using these commands, I don't get the appropriate orientation. Can you please guide me if this is an error related to how I am creating the binary file or is it related to my usage of vdfcreate command. Thanks, Bhishek.
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November 28, 2018 - 9:39am
clyne

Unforunately vapor does not allow you to change the orientation. The fastest varying dimension in your multidimensional arrray is always the X coordinate. The next fastest is Y, and then Z. To change the ordering you would have to transpose your data prior to translating into the VDC format.

jc

 

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