Modified version of GBToolbox availability

[sgbaird]

Hi Yu Feng,

In the README, it says "Figures are plotted by a modified version of Krzysztof Glowinski's GBToolbox." Upon downloading and looking at the options for GBToolbox, it doesn't seem like there's an easy way to plot a property other than the character distribution, but I could be missing something. However, I'm having trouble getting access to the documentation via this publication:

1. K.Glowinski and A.Morawiec, A toolbox for geometric grain boundary characterization, In: Proceedings of the 1st International Conference on 3D Materials Science, ed. by M. De Graef, H.F. Poulsen, A. Lewis, J. Simmons, G. Spanos, pp.119-124, Wiley (2012).

Is plotting the GBE specific to the modified version you used? If so, is that modified version available?

Thanks, and nice work on the TJ2GBE project.

Sterling

EDIT: it turned out there was some documentation in the GBtoolbox .zip file; however, the example output from TJ2GBE 'Cub.gbdat' doesn't seem to be recognized. For "quantitative analysis of GB datasets", it produces an I/O error dialogue box, and for "Characterization of GBs in datasets" almost everything is grayed out, including the "Reprocess" button.

[sgbaird]

Upon using the code, I'm beginning to think that in the output/ .gbdat file, the last column "area" is actually the GBE (J/m^2), and so when it's used for plotting in GBtoolbox, it's actually the GBED and not GBCD. Is that correct?

[Yufeng-shen]

The last column "area" is indeed the GBE. However, when we plot the GBCD we sum up the area, when we plot GBED we need to calculate the average instead of the sum, so we need a modified version of GBToolbox. I need sometime to find the plotting program and get back to you.

[Yufeng-shen]

The modified GBToolbox: (it also gives me IO error for some dataset, I failed to debug that) https://cmu.box.com/s/142ihnrjfa5l9ck8vfc7zppahib97dau

Some python code for plotting (they are pretty messy, but I hope they offer some kind of help): https://cmu.box.com/s/nvawfj5d61b7lwb5n9g2wztyjbnd2369 https://cmu.box.com/s/zrkv5pcea8x3b447od4pul9kj9nn0fie

[Yufeng-shen]

Another option (recommended) is to contact Prof. Rohrer, he has some Fortran codes can do the plotting job

[sgbaird]

Ok, thank you for looking into it. I'll explore some of those options.

[sgbaird]

I noticed a difference in the headers between a randomly generated .gbdat file and the TJ2GBE Cub.gbdat output. think the issue is that lines 3-5 need to have the hashtag # removed. Cub.gbdat (old)

# This file was created by GBToolbox 1.1.20151207
# It contains boundary parameters imported from DREAM.3D output files
# EXP
# m-3m
# L_PHI1 L_PHI L_PHI2 R_PHI1 R_PHI R_PHI2 ZENITH AZIMUTH CORRELAT AREA
...

Cub.gbdat (new)

# This file was created by GBToolbox 1.1.20151207
# It contains boundary parameters imported from DREAM.3D output files
EXP
m-3m
L_PHI1 L_PHI L_PHI2 R_PHI1 R_PHI R_PHI2 ZENITH AZIMUTH CORRELAT AREA
...

Although, I'm still working on figuring out how to generate the .dist file required for plotting.

EDIT: For getting the .dist file, Toolbar: Modules --> Analysis of GB datasets --> Quantitative Analysis of GB datasets Or click this icon:

choose .gbdat file, then click on button next to "Distributions of boundary planes for fixed misorientations" for the dialogue box to generate the .dist files for plotting.

[Yufeng-shen]

have you managed to get the plots? If the head is the issue, I will correct my python script. Or you can make a pull request if you prefer

[sgbaird]

Not yet unfortunately. I was able to generate the .dist files as above, but the last column ends up with a question mark character ? instead of a numeric value (e.g. 1.0421) occasionally. So, not sure what the issue is. It seems to run just fine through a fresh (unmodified) copy of GBtoolbox (though obviously this treats the last column as Area and not as GBE). Also, if I generate a random .gbdat and corresponding .dist file using the unmodified GBtoolbox and then plot in the modified GBtoolbox, it's fine (again, not actually GBE values). I think I'll come back to this one later.

Also, I only downloaded the single .jar file that you linked to, since I think it runs stand-alone.

[Yufeng-shen]

I tested it myself, I guess I find the reason. Those question marks means in that region we do not have data value for GBE (the input file triples.dat doesn't cover that region). In the unmodified GBToolbox it calculates the sum, which would be 0, so no problem; but in the modified GBToolbox, there is no average value can be calculated. When you generate a random .gbdat, I guess the GB distribution is more uniform, so no such problematic region.

[Yufeng-shen]

The possible solutions are:

1. replace the question mark with some "average" GBE value, like 1.00
2. Use a larger kernel size when generating the .dist file. For example, in my case it works when rho_m=5 and rho_p=8 for Sigma 7 misorientation (38.21 degree around [111] direction)

[sgbaird]

I ended up using suggestion 1 for the data I was working with and that seemed to fix the issue. I was also able to repeat suggestion 2 for the Cub.gbdat dataset and get the plot. Thank you!

[gr20cmu]

here is an update to GBToolbox: https://github.com/kglowins/gbtoolbox-legacy