accessible_volume

Accessible volume using LAMMPS

The scripts in this folder can be used to estimate the acessible volume inside a nanotube using LAMMPS.

The idea is to insert a probe (Ne atom) hundreds or millions of times to perform a Monte Carlo integration, similar to what is performed in the common exercise of estimating the value of pi. The accessible volume is determined by the Lennard-Jones interaction energy: if the energy is lesser than zero, the probe is in, if the energy is positive the probe is out of the accessible volume. This idea was previously explored in this reference.

First, you need to generate a sequence of random rumbers to be used as seed for each insertion in LAMMPS. To generate the seeds, run the python script as below, replacing NSTEPS with the number of steps you wish to use in your MC integration:

python gen_rand_ints.py NSTEPS > rngs.txt

Note that the seed should be >= 1, so beware if you generate the seeds using another method.

With the seeds in hand, open your LAMMPS topology file containing the nanotube and edit a few things:

1. Make sure your NT does not wrap around PBCs. You'll have to edit the volume.in with the origin (axis) of the NT, but if it is 0.0 0.0 0.0 and your box start at 0.0, you'll get a wrong volume.
2. Add an extra atom type (replacing X with the correct number), and attribute the following parameters to it (Ne atom):

Masses
  X  20.180  # Ne
Pair Coeffs
  X 0.0694  2.78  # Ne

Then, you should edit the volume.in (or volume_box.in for non-cylindrical NTs) file with the proper parameters. The lines you need to change are the ones that are with an "ATTENTION" comment:

1. You'll need an estimative of the NT radius (use an upper bound), in which the probe atoms will be inserted.
2. Set the number of MC steps (should be the same NSTEPS used in the python script above or lower)
3. Adjust the axial direction accordingly (in the example it's z).
4. Use the proper topology filename in read_data
5. Basically, look for ATTENTION in the file and fix it.

An example is provided in the example folder. The resuls are shown at the end of the output file as:

------ Accessible volume info ------

Number points inside = 4248
Number points outside = 5752
Cylinder radius = 5
Cylinder length = 152.2749939

Cylinder volume (A^3) = 11959.6500540418

Acessible volume (A^3) = 8832.50928886814

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