question about ReaxFF bond information

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1

Dear all,

I used fix bond/reax commend to get the bond information.

I don't understand some part of this.

Even if the bond order is zero, the connectivity info shows that it is connected. As you can see the bottom line, #9 atom is connected with #1 atom, although the bond order is zero. Is this normal? So when I draw the result, should I draw the molecule based on the bond order (above 0.3 bond order), not the connectivity?

# Max number of bonds per atom 9 with coarse bond order cutoff 0.300
# Particle connection table and bond orders
# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q
  9 3 6 1 2 10 3 7 6 0 0.000 2.999 0.456 0.000 0.228 0.015 3.698 1.000 0.771
  1 1 7 9 2 10 8 3 5 4 0 0.000 0.421 2.915 2.999 0.000 0.000 0.000 6.335 -1.000 -2.453
  2 1 7 9 1 10 8 3 7 6 0 2.999 0.421 2.915 0.000 0.000 0.000 0.000 6.335 -1.000 -2.451
  10 3 7 9 1 2 8 3 7 4 0 0.456 2.915 2.915 0.456 0.000 0.000 0.000 6.742 0.000 1.806
  8 3 6 1 2 10 3 5 4 0 2.999 0.000 0.456 0.000 0.015 0.228 3.698 1.000 0.772
  3 1 9 9 1 2 10 8 7 5 6 4 0 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.001 0.002 2.000 0.191
  7 2 4 9 2 10 3 0 0.228 0.000 0.000 0.001 0.229 0.000 0.315
  5 2 3 1 8 3 0 0.000 0.015 0.000 0.015 0.002 0.368
  6 2 3 9 2 3 0 0.015 0.000 0.000 0.015 0.002 0.368
  4 2 4 1 10 8 3 0 0.000 0.000 0.228 0.001 0.229 0.000 0.315

Thanks for your help

2

I'll let Aidan answer this ...

Steve

3

This file prints out all bonds stored by ReaxFF. These have bond-orders
greater than the cutoff, usually 0.001. ReaxFF also shifts all bond-orders
by the cutoff, so bonds just above the cutoff have bond-orders very close
to zero.

4

I misspoke. The file should only contain bonds with bond-order greater
than cutof3, which is hard-coded to be 0.3. So, I can't explain the
zeroes. Can you send me a small example?

Aidan