User Tools

Site Tools


exercises:2016_ethz_mmm:t_melting

This is an old revision of the document!


Determination of the melting temperature of a LJ system

TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:

you@eulerX ~$ module load courses mmm vmd

you@eulerX ~$ mmm-init

REMEMBER: this is the command to load the module for the cp2k program:
you@eulerX ~$ module load new cp2k

and to submit the job:

you@eulerX ~$ bsub < jobname

In this exercise, we will use a slab geometry (without vacuum region, so without a surface) with full periodic boundary conditions to study the melting behavior of nobel gases.

  • Download the 5.1 exercise into your $HOME folder and unzip it:
you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2016_ethz_mmm:exercise_5.1.zip
you@eulerX ~$ unzip exercises:2016_ethz_mmm:exercise_5.1.zip
you@eulerX ~$ cd exercise_5.1
All files of this exercise (all inputs and scripts are commented) can be also downloaded from the wiki: exercise_5.1.zip

Before you run any simulations you should do the following things:

  • Chose the nobel gas that you would like to study and find corresponding parameters for the Lennard-Jones potential here: http://arxiv.org/pdf/cond-mat/0607535.pdf
  • Prepare the simulation cell and fulfill it with the atoms of chosen gas.

To do the last step you can use the template provided in the exercise folder (111_unit.xyz). The file contains positions of dummy atoms (named with X) in the unit cell oriented along [111] axis. All the positions are given in the units of first neighbor distance. Therefore you should rescale the unit cell using the correct first neighbor distance for your nobel gas and change atom names from X to the one you have chosen. Use the following command to do it (FND and ELEMENT must be changed by approximate first neighborg distance and element type respectively):

you@eulerX exercise_5.1$ m_xyzrescale FND <  111_unit.xyz | sed 's/X/ELEMENT/' > ELEMENT_unit.xyz 

Open the file cell.inp and specify all the missing settings indicated as X. Unit cell parameters will be given you in the second line of freshly created file ELEMENT_unit.xyz. Now it is time to do the fist simulation, which is an optimization of the unit cell:

you@eulerX exercise_5.1$ cp2k.popt -i cell.inp -o cell.out
Pay attention at the folowing line in the cp2k input file:

MULTIPLE_UNIT_CELL 4 2 2

And note:

  • Initial geometry will be larger then the provided one by factors of 2, 2, and 4 in X, Y and Z directions respectively
  • There are two such lines in the input file, and both are necessary.
  • Now, run the first simulation, that should melt your system:
you@eulerX exercise_5.1$ cp2k.popt -i half.inp -o half.out

It is a 3000 step molecular dynamics. While it is running you can complete the first assignments.

  1. Take a look at the file 111.xyz with vmd. Visualize it on the screen, and try to reproduce the figure similar to the one on the last slide of the lectures of today. Include the pbc box, create a representation with vdw, periodic images, rotate the sample, etc. Produce a snapshot and include the file in your assignment.
  2. Take a look at the half.inp file. How is the temperature controlled? Are all particles moving? Why? Which are the relevant sections for MD? Which kind of MD is it?
  3. Plot the -growing- half*ener file with gnuplot. How is temperature changing? Is there a conserved quantity?
  • At the end of the first dynamics (hint: tail -f half*ener) , you can examine the half-pos-1.xyz file by performing z-profiles using the script doprof:
you@eulerX exercise_5.1$ ./doprof half-pos-1.xyz 

The script calls the histogram script of last time, with a modification: a running window of configurations is averaged to produce a single frame. First, step 1-10, then step 10-20, and so on. At the end, the file movie.half-pos-1.xyz.gif, an animated gif is produced. If it works, you can run the command:

you@eulerX exercise_5.1$ animate -loop 0 -delay 100 movie.half-pos-1.xyz.gif 

or download the file to your local machine and open in your internet browser. It will run the animation.

  1. Describe the profile you have obtained. What do you see?
  • Now, starting from the restart of this simulation, we equilibrate the system in nve, and we move all particles:
you@eulerX exercise_5.1$ bsub cp2k.popt -i 1400nve.inp -o 1400nve.out

The resulting configuration (check) will be an equilibrated system (which profile?).

Now we have a file called “1400nve-1.restart”. Do not delete it !!! It will be used as a restart file for all simulations.

SIMULATIONS AT DIFFERENT TOTAL ENERGIES FOR DETERMINING THE MELTING TEMPERATURE

As explained in the class, we will run NPE (that is, constant energies but variable cell) simulations at energies which are above and below the supposed “melting energy” (energy corresponding to melting temperature).

THE TEMPERATURE WILL NOT BE CONTROLLED DURING THE RUN

For EACH temperature you should:

  • Copy the files TEMPnpe.init.inp and TEMPnpe.inp into 1300npe.init.inp and 1300npe.inp (for T=1300) and then edit them in the appropriate points: PROJECT name, INITIAL temperature and RESTART filename.
  • Run the first simulation: bsub cp2k.popt -i 1300npe.init.inp > 1300npe.init.out ; This is a very short simulation to set the temperature using the old velocities. Why do you need it?
  • Run the second simulation: bsub cp2k.popt -i 1300npe.inp > 1300npe.out
  • Observe the temperature and the z profile. Can you find the melting temperature? How do you choose temperatures?

And finally…

  • What is the melting temperature of copper that you have found using this potential?
exercises/2016_ethz_mmm/t_melting.1460070244.txt.gz · Last modified: 2020/08/21 10:15 (external edit)