Lecture notes

Lecture notes

Your first Atomify Lammps simulation

Open your First simulation using Atomify Lammps

• While the simulation runs
  • what phases of matter do you see in the simulation?
  • try to change the view of the simulation
    • letters on keyboard:
      • Q/E: up/down
      • A/D: right/left
      • W/S: zoom in/out
    • using touchpad on Mac:
      • 2 fingers up/down = zoom in/out
      • 1 finger clicked in and moving = rotate
      • 2 fingers clicked in and moving = move up/down/sideways.
• When the simulation ends the Console output is shown. This output is the same as written to the logfile.
  • click Analyze in Notebook
  • follow instructions and answer questions in the Notebook
• Edit the input file and repeat simulation and analysis
  • click on my-first-md-simulation.in in the leftmost menu
  • list of edits:
    1. comment the line starting with nve and uncomment the line starting with nvt to make Lammps run the simulation at constant temperature
    2. change the temperature to 0.45: fix 1 all nvt temp 0.45 0.45 0.45
    3. change the temperature to 0.6: fix 1 all nvt temp 0.6 0.6 0.6
    4. increase length of simulation
  • close the Console output window and study the configuration of atoms
    • what phases of matter do you see now?
  • Click Notebook in the leftmost menu, run the Notebook and anwer the questions
  • Edit Notebook to plot pressure as well. How does pressure change with temperature? Why?

Diffusion simulations

Here is a video about diffusion of heat and matter and a video about diffusion using MD. Finally, a video on vthe random walk as a diffusion process and on an algorithmic model of diffusion.

In these simulations, we simulate atoms diffusing in a liquid and measure the diffusion coefficient using the mean square displacement. The mean square displacement in the x-direction is defined as

\( MSD = \langle (\vec x(t) - \vec x_0)^2\rangle = \frac{1}{N}\sum_{i=1}^{N} |\vec x^{(i)}(t) - \vec x^{(i)}_0|^2 \)

and relates to the diffusion coefficient \( D \) as

\( D = \frac{\langle (\vec x(t) - \vec x_0)^2\rangle}{2t} \)

where \( t \) is the time.

• What is the ratio of diffusion coefficients of the two atom types in this simulation?
• Look in the input file 3D-msd-diffusion.in and see if you can determine why one atom type diffuses much faster than the other.
• Try to change the parameter you think is responsible for the difference in diffusion coefficient and see if you can make them equal

Melting of a 2D solid

Click on the example entitled: Melting of a 2D solid

• Observe the phases during the simulation. Which phases do you see?
• Does this correspond to what you expect from the phase diagram?
• How does the slope of the mean square displacement change for the different phases?

Heat capacity simulation

Weekly exercise

In order to make sure you reach the learning goals of this week: complete the weekly exercises of week 36.