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differentiate between these two types of oxygen atoms for machine learning simulations

Posted: Tue Feb 04, 2025 9:12 am
by aijitha_john

I'm performing AIMD simulations for a system containing two different types of oxygen atoms: one on the surface and the other outside the surface. To distinguish between them, I labeled the oxygen atoms as "O2" and "O" in the POSCAR file. However, I received the following warning:

"WARNING: type information on POSCAR and POTCAR are incompatible. POTCAR overwrites the type information in POSCAR. typ 3 type information: O2 O."

Is there an alternative way to differentiate between these two types of oxygen atoms for machine learning simulations?


Re: differentiate between these two types of oxygen atoms for machine learning simulations

Posted: Tue Feb 04, 2025 9:34 am
by alexey.tal

Dear aijitha_john,

Thank you for your question.

It is important that the types in your POSCAR match the types in POTCAR. So if you now have two oxygen types in your POSCAR, you need to have the same in your POTCAR, i.e., copy the oxygen potential twice.

Best wishes,
Alexey


Re: differentiate between these two types of oxygen atoms for machine learning simulations

Posted: Tue Feb 04, 2025 11:45 am
by aijitha_john

Thanks Alexye,

My POSCAR is like

Title
1.0000000000000000
18.1506171891947687 0.0000000000000000 0.0000000000000000
-9.0753085945974004 15.7188955799581809 0.0000000000000000
0.0000000000000000 0.0000000000000000 25.0000000000000000
C F O2 O Ti
72 36 72 36 107
C
.....

and

grep TITEL POTCAR
gives:
TITEL = PAW_PBE C 08Apr2002
TITEL = PAW_PBE F 08Apr2002
TITEL = PAW_PBE O 08Apr2002
TITEL = PAW_PBE O 08Apr2002
TITEL = PAW_PBE Ti_sv 26Sep2005
I have copied POTCAR for Oxyge twise. Is there any specific keyword I need to add or modify to correct this issue?


Re: differentiate between these two types of oxygen atoms for machine learning simulations

Posted: Tue Feb 04, 2025 12:21 pm
by alexey.tal

What version of VASP are you using? The newest version of VASP can ignore the suffix in the species type, so it should not show this warning. In the older versions, you should specify species as O, not O2. But in principle it is a warning so you will still get the correct results as the elements in your POSCAR and POTCAR indeed match. This warning just means that in this version of VASP type O2 was not correctly interpreted.


Re: differentiate between these two types of oxygen atoms for machine learning simulations

Posted: Tue Feb 04, 2025 12:32 pm
by aijitha_john

I am using vasp version 6.4.3


Re: differentiate between these two types of oxygen atoms for machine learning simulations

Posted: Tue Feb 04, 2025 12:37 pm
by alexey.tal

VASP 6.4.3 should be able to identify these types correctly.
Could you please share the input and output files as described in our forum guidelines?


Re: differentiate between these two types of oxygen atoms for machine learning simulations

Posted: Tue Feb 04, 2025 1:50 pm
by aijitha_john

Dear alexey,
The vasp input files are attached.


Re: differentiate between these two types of oxygen atoms for machine learning simulations

Posted: Tue Feb 04, 2025 2:14 pm
by alexey.tal

Actually, what I said above is not exactly correct. VASP ignores the suffix for elements with two characters. It simply ignores symbols after the second character. In your case the second character is 2, so it tries to match O2 and O. But you can read in the warning message that the elements that couldn't be matched are O and O2, so the results should be correct. We will try to make this string matching mechanism more intelligent.