Hello!
I am trying to simulate supercell by using replicate command but if I want to add polymers use the same dat file then polymers will also replicate. Can I use two dat files together? if yes then how?
I am using LAMMPS (29 Oct 2020) …
Please see the documentation for the read_data command — LAMMPS documentation
But I would recommend against it. Using the “add” mode has many quirks, sometimes unexpected (but documented) behavior, and puts many constraints on the data files. This makes it difficult to be used correctly, especially for inexperienced LAMMPS users. I would rather recommend to replicate and combine geometries before creating a data file and then build just one data file with the final geometry. The tools used for those processes are usually much more suitable for such kind of manipulations than LAMMPS itself.
But when I replicate my MOF some of the atoms are overlapped is it possible to delete overlapped atoms ?
Yes, the delete_atoms command can do that. However, that overlap is an indication that your original data file is bogus and either has atoms in the wrong places or box dimensions that do not fit the geometry. So rather than deleting the overlapping atoms, you should fix the original data file to be proper and consistent.
I want to replicate through single unit of MOF. But I am wondering that if I replicate it and I must truncate the terminals by -H or phenyl ring so how is it possible to truncate the supercell after simulation. It should be done before the simulation. Is there any way to add phenyl ring and at the same time replicate it in order to avoid overlapping of atoms?
The replicate command will just do what its documentation says it does. It knows nothing about polymers and how to connect or terminate them. This usually requires creating the geometry and connectivity with an external software for the entire system and then converting or transferring that information to a LAMMPS data file.