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.

Weekly exercise

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