How to change atom types for selected atoms

[Joonho Park]

Hi, guys

I want to change color or anything for a certain atoms e.g. inserted oxygen atoms while there are oxygen atoms already in the crystal. So, I need to change atom type for a group of atoms. Is this possible?

Thank you for your time.

Joonho

School of Electrical Engineering, KAIST

cp: +82-10-3645-4218

office: +82-42-7623

mailto: hope...@kaist.ac.kr

Senior Researcher

[KK M]

yes you can

see the screen shots

1st one

now changed color of the purple now to say red. click the arrow show color dot and change whatever you want

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[Joonho Park]

Hi, KK,

Thanks for your reply.

But as your example shows, it can change only one atom at a time. This is not efficient. If I need to change so many POSCAR files, I can not change color in all the files.

As shown in the figure, there is grouping for the same kinds of atoms. Below is the only recipe I have found.

Firstly, as for the atoms with different color, make a different type. So, I have changed POSCAR

from Mo S O or Mo S O O to Mo S O Oa (Note that O1, O2 are not working)

Then vasp shows different atom groups with Oa for several atoms. Then, oxygen atoms under Oa can change color at one operation.

To automatically assign color, find elements.ini in VESTA installation directory and add new atoms type with color there. So, I have copy O atom line to the last line and add color also 

94 Pu  1.64  2.16  0.860    0.30000    0.30000    0.30000
 95 Am  1.73  2.16  0.975    0.30000    0.30000    0.30000
 96 Oa  0.74  1.52  1.400    0.00000    0.89804    1.00000

This is the copied line of O atom but different color RGB values in the later three columns.

Then, whenever open POSCAR.vas with Oa atom kinds, it automatically colors Oa atoms.

This is the only recipe that I found.

Sincerely,

Joonho

School of Electrical Engineering, KAIST

cp: +82-10-3645-4218

office: +82-42-7623

mailto: hope...@kaist.ac.kr

Senior Researcher

To view this discussion visit https://groups.google.com/d/msgid/vesta-discuss/CADsoCrWbzXXn8TX1gjKK2dN3adN03ULPB4SWe%2B9WokF9oLY%2B3g%40mail.gmail.com.