Please see the forum guidelines about how to correctly quote input scripts or any text in the forum. Significant chunks of those files are unreadable.
Those are two very different models. The first is using an atomistic description, the second is a grid free mesoscale model (where the positions do not represent individual atoms). These models differ massively in scale and resolution.
You really need to have an in-depth discussion with an adviser or tutor or competent collaborator. You need a much better understanding of the physics and what models can be used for what purposes. This is near impossible to teach online and specifically difficult in a forum discussion. Also, this is - as stated before - off-topic for the LAMMPS categories. While you are quoting LAMMPS inputs, your question has nothing to do with LAMMPS itself, but is about the models (so you could use just any other simulation code that has support for either model).
You are comparing apples and oranges here. Either model is valid for what it is supposed to be used for and within the error ranges for what they are parameterized for and that are intrinsic in those models, but since they are very different models and applied to significantly different problems and problem sizes, you cannot compare them.