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+download LAMMPS [lammps-23Jun2022.tar.gz](https://download.lammps.org/tars/lammps-23Jun2022.tar.gz) St. Joan edition here (version used in this study)
+
 # Introduction
 
 LAMMPS is a classical molecular dynamics simulation code with a focus in materials modeling.
@@ -14,13 +16,24 @@ 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
 
-# Algorithm
+# Algorithm and Data structures
+
 
+FIXME neighbor
 LAMMPS computes interactions between atoms.
-If a pair of atoms is "close" (within the *pair_style* cutoff distance), it produces a *short-range* interaction in "real space" and is computed using a *pair_style*.
+If a pair of atoms are "neighbors" (that is, they are placed  the *pair_style* cutoff distance), it produces a *short-range* interaction in "real space" and is computed using a *pair_style*.
 If atoms aren't within the cutoff distance, these become *long-range* interactions in "reciprocal space" (FFT domain).
 The `PairLJCharmmCoulLong::compute` computes short-range interactions.
 
+File `neigh_list.h` contains the `int **firstneigh` array.
+Note that the `**` denotes that it is a double pointer or pointer to pointer.
+In other words, `int **firstneigh` is a pointer to an array of pointers to arrays of `int`.
+
+`firstneigh[i]` contains an array of the 
+
+atom_vec.h -> contains `**x` and `**f` (3D)
+neigh_list.h -> contains `**firstneigh` (for each i, store array of neighbors j)
+
 LAMMPS uses 64-bit `double` precision numbers for floating point calculations and 32-bit `int` numbers for integer computations.
 This can become somewhat of an issue with the `jlist` array, which is an array of `int`s which act as indexes of `x` and