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String Calculation Visualisation of Images

PostPosted: Thu Jan 10, 2019 10:12 am
by woffermans
Dear ABINIT friends,

There is a nice tutorial about a STRING calculation https://www.abinit.org/sites/default/fi ... tring.html

Unfortunately, the tutorial does not mention how to visualise the images and even better the evolution of the ``string of images`` during the optimisation. This is a big deficit to my opinion.

If I run a STRING calculation, several *_IMG* files are generated, for example pdo_IMG5_GSR.nc. It is not clear how to extract the ion positions out of this file.

Can someone give me a hint on how to achieve the visualisation of the generated images?

Even better, can the tutorial be updated with this information? A link to another source would already be sufficient.

Re: String Calculation Visualisation of Images

PostPosted: Wed May 08, 2019 3:31 am
by ketong
Hi woffermanns,

I think you can use VESTA/OVITO/VMD to visualize the string calculations. If you want to use them, you need to convert the *_GSR.nc to supported format by them. At this time, Abipy is your friend. You can get detailed information from https://github.com/abinit/abipy.

VESTA can visualize every image conveniently. It supports poscar and xsf format. (Note: the file name must be POSCAR or .xsf, because VESTA identifies the format according to the name.) The detailed information can be seen from http://jp-minerals.org/vesta/en/.
OVITO and VMD also support POSCAR format. In addition, they can create a movie using these image files. Please see these websites to get more information: https://ovito.org/, https://www.ks.uiuc.edu/Research/vmd/.

I hope this information is useful to you.