|
|
|
*
|
|
|
|
|
|
|
|
# Introduction
|
|
|
|
|
|
|
|
LAMMPS is a classical molecular dynamics simulation code with a focus in materials modeling.
|
|
|
|
It is written using C++.
|
|
|
|
The most object-oriented aspects of C++ are used at a high-level to help structure and organize the code, while critical kernels are written using C-style code.
|
| ... | ... | @@ -12,3 +16,8 @@ The input contains two files: |
|
|
|
- `pair_style lj/charmm/coul/long 8.0 10.0` This is the line that specifies that we are using the *lj/charmm/coul/charmm* *pair_style*. If a different *pair_style* was selected, then `PairLJCharmmCoulLong::compute` would not be executed, and the optimizations would not have any impact. Moreover, the `8.0`and `10.0` represent the *cutoff distances*, which can have an impact to the execution of the function. For more information, check the LAMMPS [documentation](https://docs.lammps.org/pair_charmm.html#pair-style-lj-charmm-coul-long-command).
|
|
|
|
- `data.protein`: contains the initial data for the atoms in the simulation and their properties
|
|
|
|
|
|
|
|
LAMMPS computes interactions between atoms.
|
|
|
|
If the atoms are "close" (within the *pair_style* cutoff distance), these are *short-range* interactions in "real space" and are computed using a *pair_style*.
|
|
|
|
If the atoms aren't within the cutoff distance, these are *long-range* interactions in "reciprocal space" (FFT domain).
|
|
|
|
The `PairLJCharmmCoulLong::compute` computes short-range interactions.
|
|
|
|
|
