Add info on LJ parameters used, and set cutoff distance in relation (#…

…202)

doc/examples/integrator_validation.ipynb

@@ -53,7 +53,7 @@
    "id": "930ae351",
    "metadata": {},
    "source": [
-    "The example system consists of 1000 Lennard-Jones (LJ) particles simulated under NVE conditions. To illustrate how the integrator convergence validation can pick up small errors in the simulation, the simulation were repeated with different interaction cutoff schemes. In all cases, the LJ interactions were discarded if the particles were more than 1 nm apart. Uncorrected, this leads to a small discontinuity in the potential and the force at the cutoff distance. A first approach to correct this discontinuity is by shifting the potential by a constant value such that it reaches 0 at the cutoff distance. This fixes the discontinuity in the potential, but does not alter the forces. A second approach is to smoothly switch off both the forces and the potential such that both reach zero at the cut-off distance.\n",
+    "The example system consists of 1000 Lennard-Jones (LJ) particles simulated under NVE conditions. The system uses Argon parameters σ = 0.3345 nm and ϵ = 1.045128 kJ/mol ([White 1999](https://doi.org/10.1063/1.479848)). To illustrate how the integrator convergence validation can pick up small errors in the simulation, the simulation was repeated with different interaction cutoff schemes. In all cases, the LJ interactions were discarded if the particles were more than 1 nm (≈3σ) apart. Uncorrected, this leads to a small discontinuity in the potential and the force at the cutoff distance. A first approach to correct this discontinuity is by shifting the potential by a constant value such that it reaches 0 at the cutoff distance. This fixes the discontinuity in the potential, but does not alter the forces. A second approach is to smoothly switch off both the forces and the potential such that both reach zero at the cut-off distance.\n",
     "\n",
     "The integrator validation analyzes the convergence of the fluctuations around the integrator constant of motion. For a symplectic integrator, the fluctuation is expected to be directly proportional to the square of the time step. The `physical_validation` check calculates the fluctuation convergence from multiple simulations with different time steps and validates the expectation."
    ]