Dear lammps users,
I am trying to study the effect of linked list size and qeq on the performance of NVE ensemble in lammps.
But for doing this I need to change the short ranged linked list cell size and qeq tolerance values.
I know how to change qeq tolerances, because that is an argument to qeq fix. But I do not know how to increase or decrease the linked list cell size in lammps. Is there a parameter in the code that controls it, or some command that can vary it.
I do not know how to do this and I do not want to change the code in any respect, as I do not understand how the reax/c flow of control is and how the code is implemented.
Reax/c builds its own neighbor list from LAMMPS’ main neighbor list. The cutoff of this neighbor list (which is usually 10 angstroms) is defined in its potential files. This is done in write_reax_lists in pair_reax_c.cpp.
Then additional neighbor lists are built from this reax/c list, including the short range (aka bond order) and hydrogen bond lists. The cutoffs for bond order and hydrogen bond lists are set to default values of 5.0 and 7.5 angstroms, respectively. You can change these cutoff lengths a the control file in the pair_style command (see reax/c doc page: http://lammps.sandia.gov/doc/pair_reaxc.html)). Changing the bond order cutoff is what you are looking for.
Lastly, changing cutoffs is effectively changing the parameterization – so please know what you are doing.
Thank you very much for your reply. I do not understand how changing nearest neighbour cutoff will change the parameterization as cut off is defined based on the parameter for Bond Order Sigma in reaxff. But lammps, I think does not use that convention to define the maximum allowable bond distance.
And it allows users to define what they want as their value, which I think is fine, since this value will only define how the linked list cell are created and what their sizes are.
How will changing nbrhood_cutoff will change the reaxff parameterization. Is there something else which I am missing?
Thanks for your suggestions, it helped me to solve the problem.
I misread your first email: short range neighbor list and “linked cell” list are two very different things. Short range neighbor list in reax/c is the bond order neighbor list, while linked cell is an algorithm LAMMPS uses to build its main neighbor list. Check out neigh_modify doc page for changing linked cell bin size: http://lammps.sandia.gov/doc/neigh_modify.html.
Changing the bond order cutoff could change the number of neighbors around atoms, which could effectively change the interatomic interactions. Reax/c has this option to change bond order cutoff mainly for the reason of adapting to different parameterizations (for different materials), not for users to change it freely.