Greater atom connectivity error

GULP
1

Dear Prof Gale,

I’ve written a GULP input file for a cubic supercell in which I have specified the connectivity between all atoms connected with harmonic bonds. For example, I have used lines such as this for each connection:

connect 111 211
harm bond
Zr111 Zr211 2.376 12.946

where I have left out the label since the default, as I understand it from the user manual, is to take the nearest neighbour atom of that label anyway. My three body potential lines look like this:

Zr232 Zr242 Zr231 9.15 90.0000000

However when I try to run GULP with my file I get the following error messages:

ERROR : Atom number in connectivity is greater than number of atoms
Program terminated by processor 0 in reorder

I have checked to make sure that any atoms specified in the connections section of the input file are previously listed in the coordinates section, so I am not sure why there seems to be an issue with the atom numbers. I have also made sure that no interactions are double counted.
I’d be very grateful if you could suggest what might be going wrong in my input file that prevents GULP from running it.
Many thanks,

Robert

2

Hi Robert,
I really need to see your input to be able to work out what’s wrong, beyond the obvious of not enough atoms in the coordinate section. It’s important to remember that if you’ve used the “supercell” option then you can’t specify the connectivity for atoms that aren’t in the original cell since they aren’t there when the option is read for the initial cell. If you want to specify the connectivity for the supercell then you’d need to build this first and then create a new input. That’s my only guess without seeing your file.
Regards,
Julian

3

Hi Julian,

Thank you for getting back to me so quickly. I think I have since resolved the issue - I wrote in the image labels in the connectivity section rather than not including them and now I am getting the output I was after.
Kind regards,

Robert