separate template for uncharged lammps to increase the speed

[nasimanousheh]

@jadhao and @kadupitiya

• The template and input data file for charged and uncharged surfaces are separated. This increases the speed of simulation for uncharged case.
• I updated the examples for uncharged lammps. If you compare the energy values of old uncharged lammps with new one, the values are not exactly the same (in old example, all values are based on 5424 particles and epair (vdw + coulomb) is not added. In new version, all output is based on 424 particles and the values of 8th column is epair. The energy of epair in new version is matched with inhouse.

[jadhao]

@nasimanousheh how fast is the uncharged simulation in LAMMPS now -- same speed as before? and how does it compare to inhouse code for the same choices of parameters? what timestep are you using in both inhouse and LAMMPS?

[jadhao]

@nasimanousheh i would have expected the density profiles to be exactly the same as the old examples (with 5k total particles), are they not? energies can change for reasons you say, but density profile change is not expected.

[nasimanousheh]

• The speed is the same as before we introduced the charge on surface.
• The time step (0.001) and all other parameters are not changed and are the same in both inhouse and lammps.
• The values of density profile are not exactly the same as old version (numerically), but they are matched. I think the reason they are not exactly the same is that in old version we increased the confinement size a bit (-(0.5 * lz) - pow(10.0,-4)) to let the mesh points be inside the cell box. In new version, there is no need to increase the confinement size. This changes the coordinates of ions: for old version: ITEM: TIMESTEP 1100 ITEM: NUMBER OF ATOMS 424 ITEM: BOX BOUNDS pp pp ff -1.0728100000000000e+01 1.0728100000000000e+01 -1.0728100000000000e+01 1.0728100000000000e+01 -2.1009400000000000e+00 2.1009400000000000e+00 ITEM: ATOMS id type q x y z 10 1 8.86201 -7.84572 -7.87987 0.0220472 for new version: ITEM: TIMESTEP 1100 ITEM: NUMBER OF ATOMS 424 ITEM: BOX BOUNDS pp pp ff -1.0728100000000000e+01 1.0728100000000000e+01 -1.0728100000000000e+01 1.0728100000000000e+01 -2.1008399999999998e+00 2.1008399999999998e+00 ITEM: ATOMS id type q x y z 10 1 8.86201 -7.84592 -7.87969 0.0218927