Dear Dr. Axel Kohlmeyer,
Hello Dr. Kohlmeyer and thank you so much for your many response to my inquires.
I was curious if I could ask a question regarding the create_bonds command.
I have a line in my script which specifies: create_bonds many mol mol 1 0.85 1.3
I have a collection of type 2 atoms named as “mol” which I would like to add bonds to form these Type 2 atoms into polymer chains. From reading the manual, I understand that the bonds will be created if the distance between atoms fall in the range of 0.85 to 1.3. Moreover, the added bonds will be specified as Type 1 bonds.
I received the following error when running my simulation: New bond exceeded bonds per atom in create_bonds
I have specified “extra/bond/per/atom 2” in my read_data command, and I am implying that more than 2 neighboring atoms (candidates) exist that fall within the minimum and the maximum distance such that more than 2 bonds will be formed for a single atom.
Since I would like to stick with using the keyword “many,” I was curious if there is a way to restrict the creation of the bonds to 2 bonds per atom regardless if there are many surrounding candidates that satisfy the distance criteria.
If not, I was curious if I am left to specify an arbitrary number for “extra/bond/per/atom” that is large enough that no new bonds could possibly exceed the specified value.
Thank you so much for your time.
Sincerely,
Masato Koizumi