error: All the point atoms are classified as surface atoms

[akareem28]

Hi Sir,
I am trying to calculate the Voronoi polyhedra of propanol-ethanol binary mixture. Since I am interested in calculating the polyhedra formed by the hydrogen bonding, I have taken only one atom type (i.e., oxygen atoms alone), in the input script I have given the cutoff radius as 3.5 (A), which has been taken from the minima of rdf. the atomic radius for oxygen atom is 0.6 (A). While running the vorotis code getting an error: All the point atoms are classified as surface atoms. Since the cutoff distance is valid, there are oxygen atoms with a distance less than 3.5, which I also verified visualluy using VMD software. Could please help me in figuring it out where the error came from. I have attached the lammps dump file and the input script for the reference.
voronoi_ps3.txt
dump_propanol_80lammpstrj.log

[vorotis]

Hi akareem28,

Thank you for your inquiry.

As you mentioned, the calculation was failed when I set cutoff.radius to be 3.5.
However, when I set cutoff.radius to be 15, the calculation was normally finished.
This means that the shortest distance for type-1 atoms is larger than 3.5.
The atoms you think are oxygen atoms may not actually be oxygen atoms.

Best regards,
Kengo Nishio

[akareem28]

Hi Sir, thank you for the reply,
The atom type 1 given in the dump file is oxygen atoms, I used the same atom type number here also. there are oxygen atoms with a distance of less than 3.5 (A), which I also verified visually using VMD software. Is there any other thing that I have missed?

[vorotis]

Hi akareem28,

I apologize that I could not reply earlier.

My previous reply was insufficient.

To make the Voronoi polyhedron of atom i, at least more than 4 atoms need to exist within a sphere of a radius of 3.5 placed at the center of atom i. Since no type-1 atoms meet this condition, no Voronoi polyhedra are made and all the point atoms are classified as surface atoms.

Best regards,
Kengo Nishio

[akareem28]

Thank you sir for your response.

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On Mon, 31 Jul, 2023, 14:16 Kengo Nishio, ***@***.***> wrote: Hi akareem28, I apologize that I could not reply earlier. My previous reply was insufficient. To make a Voronoi polyhedron of atom i, at least more than 4 atoms need to exist within a sphere of a radius of 3.5 placed at the center of atom i. Since no type-1 atoms meet this condition, no Voronoi polyhedra are made and all the point atoms are classified as surface atoms. Best regards, Kengo Nishio — Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANQDRA6YIE2FGV4VQKQEUY3XS5WHNANCNFSM6AAAAAA2VEFAQE> . You are receiving this because you authored the thread.Message ID: ***@***.***>