Regarding visualization of the bond-order parameter 'q6' obtained by the compute hexorder/atom

Hey all,

I dumped all the q6 values, x, y, z too, in a dump file ‘output.hexorder’. The q6 values had a real and imaginary part presented in 2 columns in the output file. I opened the file in excel, found the absolute value of q6 and replaced the first column (real part) with the absolute values. I didn’t change the file extension. When I use Ovito to open the file, it says the file type is not supported. But it opens the initial file without the modification done!
What am I doing wrong?


I don’t know. It sounds more like an Ovito Q.


Maybe Ovito is picky about the whitespace used (tabs vs. 1 space vs. many spaces)?

Yes, this is not really a LAMMPS problem. It sounds like an interaction between Ovito and some kind of modification to white space or line breaks introduced when you saved the file in Excel. You could verify this by opening the original sump file in Excel and saving it again. Depending on how you do that, you may be able to avoid the problem.

I will also mention that you can easily have LAMMPS dump the absolute value of q6 for you:

compute q6 all hexorder/atom

variable normq6 atom sqrt(c_q6[1]^2+c_q6[2]^2)
dump 2 all custom 1000 hexorder.dump id c_q6[1] c_q6[2] v_normq6