To whom it may concern,
I am simulating a bulk system of water molecules using the REAX/C package in LAMMPS. For the post-processing of data which I want to do, I need to know the potential energy between each pair of molecules, i.e. for a system of 1000 water molecules this would be a 1000 x 1000 matrix. I could calculate the same information even if I had the interaction potential energy between each pair of atoms in the simulation, i.e. for the same system above this would be a 3000 x 3000 matrix. I’ve tried the compute pe/atom, however the output of this is in fact a vector summing over all of the columns of the matrix I would like to obtain. Does LAMMPS have a command which could produce and dump this type of matrix?
If there is no such command, would you happen to know of a standalone function / code that evaluates and outputs such matrix based on the ReaxFF force field equations? I am thinking I could feed the coordinates I obtain from LAMMPS to such a function and it could give me the interatomic potential energy matrix at those time-steps.
Thank you very much!
All the best,
Filip
To whom it may concern,
I am simulating a bulk system of water molecules using the REAX/C package in LAMMPS. For the post-processing of data which I want to do, I need to know the potential energy between each pair of molecules, i.e. for a system of 1000 water molecules this would be a 1000 x 1000 matrix. I could calculate the same information even if I had the interaction potential energy between each pair of atoms in the simulation, i.e. for the same system above this would be a 3000 x 3000 matrix. I’ve tried the compute pe/atom, however the output of this is in fact a vector summing over all of the columns of the matrix I would like to obtain. Does LAMMPS have a command which could produce and dump this type of matrix?
no.
If there is no such command, would you happen to know of a standalone function / code that evaluates and outputs such matrix based on the ReaxFF force field equations?
no.
I am thinking I could feed the coordinates I obtain from LAMMPS to such a function and it could give me the interatomic potential energy matrix at those time-steps.
that “function” is effectively the code in the src/USER-REAXC folder in combination with the “rerun” command. reaxff is a complex force field with a large number of components contributing to the total interactions, including a charge equilibration scheme. if you want to decompose these contributions, you will have to modify the source code of each contribution to output the projection of interaction energy that you are interested in.
axel.