Atomic interactions

Select an interaction potential and its parameters.

Number of chemical species in the simulation

Pair interaction matrix

The interaction matrix determines which potential to use between each pair of atoms of all possible combinations of chemical species. There are as many rows and columns as there are species, and each cell in the matrix contains the interaction of type row with type column. Click on a cell and select the potential potential and its parameters on the left, until all cells appear green.

No interaction (ideal gas)

Lennard-Jones pair potential

\[ V(r)=4 \varepsilon \left[ \left( \frac {\sigma} {r} \right)^{12} - \left( \frac {\sigma} {r} \right)^6 \right] \]

$\varepsilon=$ K (binding energy)
$\sigma=$ Å (length scale, $2^{\frac16}\sigma=r_m$ is equilibrium dimer separation distance)
$r_{cut}=$ Å (all atomic interactions beyond $r_{cut}$ are ignored. recommended: $r_{cut}\approx2.5\sigma$)

Sample geometry

Select a sample geometry and boundary conditions.

Crystalline solid (face centered cubic lattice)
$d=$ (crystal size $d\times d\times d$ unit cells )
$a_0=$ Å (lattice constant)

Two elements selected. Building L1₂ ordered phase.

More than two elements selected. Building L1₂ derived ordered phase by filling the fcc unit cell.

Nano particle
$r=$ Å (radius)

Gas
$N=$ (number of atoms)
$T=$ K (temperature)
$L=$ Å (box size, $V=L^3$)

More than one element selected, but all atoms will be of type A

enforce minimum separation distance for initial state
r_min= Ang

The gas atoms are placed at random positions in the simulation box. If an interaction potential is used, a small fraction of neighboring atoms may be very close and thus in the repulsive regime of the potential. These atoms will repell eachother vigorously and accellerate very fast. This is undesired and can be avoided by checking this option.

Periodic boundaries
Volume changing piston is not available in this mode!

Reflecting boundaries

Selected sample is too dense to enforce the chosen minimum distance!
Your options are:

Retry (may help in bordeline cases)
Retry without enforcing minimum distance
Go back and retry with smaller r_min

remove heat

Simulation

T = K

P = MPa

E_pot = eV

E_kin = eV

U = eV

Calculate and display energies

Move piston
current position: z=?
v_z= Å/ps

max_z= Å, min_z= Å

The piston is implemented by moving the two box walls perpendicular to the z-axis inward with a velocity of v_z (negative v_z move the walls apart). The wall is assumed to have infinite mass and reflected particles will exhibit a momentum transfer, adding 2v_z to their velocity z-component.

Gather data Autorefresh plot
Plot vs.

Activate barostat (affecting )
P₀= MPa, τ= ps

ramp barostat setpressure
$\frac{dP_0}{dt}$= MPa/ps

A barostat controls the pressure in the simulation cell. Pressure is lowered by expanding the cell and increased by shrinking the cell. jsMD implements a Berendsen barostat.

Activate thermostat
T₀= K, τ= ps

ramp thermostat settemperature
$\frac{dT_0}{dt}$= K/ps

A thermostat controls the temperature in the simulation cell. jsMD implements a Berendsen thermostat that regulates temperature through simple velocity rescaling.

Get raw data for