exercises:2015_ethz_mmm:t_melting
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exercises:2015_ethz_mmm:t_melting [2015/02/06 17:49] – external edit 127.0.0.1 | exercises:2015_ethz_mmm:t_melting [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== Determination of the melting temperature of copper ====== | ====== Determination of the melting temperature of copper ====== | ||
+ | |||
+ | |||
+ | <note warning> | ||
+ | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
+ | |||
+ | you@eulerX ~$ module load courses mmm vmd | ||
+ | |||
+ | you@eulerX ~$ mmm-init | ||
+ | </ | ||
+ | |||
+ | |||
+ | <note important> | ||
+ | |||
+ | <code bash> | ||
+ | you@eulerX ~$ module load new cp2k | ||
+ | </ | ||
+ | |||
+ | **and to submit the job:** | ||
+ | |||
+ | <code bash> | ||
+ | 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 copper. | 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 copper. | ||
- | As usual, connect to brutus and enter the following commands: | + | |
- | < | + | |
- | module load cp2k/trunk.2.5.13191 | + | * Download |
- | module load open_mpi/1.6.5 ! THIS IS NEEDED IF YOU WANT TO RUN AN MPI PARALLEL RUN --- NOT CONVENIENT IN THIS CASE | + | < |
- | module load vmd | + | you@eulerX ~$ wget http://www.cp2k.org/_media/ |
- | mkdir EX_5.1 | + | you@eulerX ~$ unzip exercises: |
- | cd EX_5.1 | + | you@eulerX ~$ cd exercise_5.1 |
</ | </ | ||
- | <note tip>Copy into that directory the **COMMENTED** files that can be downloaded from the wiki: {{exercise_5.1.tar.gz|exercise_5.1.tar.gz}} </ | ||
+ | <note tip> | ||
+ | All files of this exercise (**all inputs and scripts are commented**) can be also downloaded from the wiki: {{exercise_5.1.zip|exercise_5.1.zip}} | ||
+ | </ | ||
- | Now, run the first simulation, that should melt your system. | + | * Now, run the first simulation, that should melt your system: |
- | < | + | < |
- | bsub cp2k.popt -i half.inp | + | you@eulerX exercise_5.1$ |
</ | </ | ||
- | It is a 3000 step molecular dynamics. | + | It is a 3000 step molecular dynamics. |
- | < | + | < |
- | | + | |
- | | + | |
- | | + | |
</ | </ | ||
- | 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** | + | * 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**: |
- | < | + | < |
- | ./doprof half-pos-1.xyz | + | you@eulerX exercise_5.1$ |
</ | </ | ||
Line 39: | Line 64: | ||
At the end, the file **movie.half-pos-1.xyz.gif**, | At the end, the file **movie.half-pos-1.xyz.gif**, | ||
- | < | + | < |
- | animate -loop 0 -delay 100 movie.half-pos-1.xyz.gif | + | you@eulerX exercise_5.1$ |
</ | </ | ||
or download the file to your local machine and open in your internet browser. It will run the animation. | or download the file to your local machine and open in your internet browser. It will run the animation. | ||
- | < | + | < |
- | A4) 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: | + | * Now, starting from the restart of this simulation, we equilibrate the system in nve, and we move all particles: |
- | < | + | < |
- | bsub cp2k.popt -i 1400nve.inp | + | you@eulerX exercise_5.1$ |
</ | </ | ||
The resulting configuration (check) will be an equilibrated system (which profile?). | The resulting configuration (check) will be an equilibrated system (which profile?). | ||
- | Now we have a file called | + | Now we have a file called |
- | **THIS WILL BE USED AS RESTART FILE FOR ALL SIMULATIONS! DO NOT DELETE IT!** | ||
===== SIMULATIONS AT DIFFERENT TOTAL ENERGIES FOR DETERMINING THE MELTING TEMPERATURE ===== | ===== SIMULATIONS AT DIFFERENT TOTAL ENERGIES FOR DETERMINING THE MELTING TEMPERATURE ===== | ||
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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 " | 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 " | ||
- | <note tip>THE TEMPERATURE WILL NOT BE CONTROLLED DURING THE RUN</ | + | **THE TEMPERATURE WILL NOT BE CONTROLLED DURING THE RUN** |
- | For EACH temperature you have to: | + | For EACH temperature you should: |
- | <note important> | + | |
- | * A5) 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. | + | * 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. |
- | * A6) 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 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? |
- | * A7) Run the second simulation: bsub cp2k.popt -i 1300npe.inp > 1300npe.out | + | * 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? | * Observe the temperature and the z profile. Can you find the melting temperature? | ||
- | </ | ||
- | |||
- | <note tip>Note that you can run several A5-A7 steps at the same time and in the same directory.</ | ||
And finally... | And finally... | ||
- | < | + | < |
- | A8) WHAT IS THE MELTING TEMPERATURE OF THIS POTENTIAL (APPROXIMATELY)? | + | * What is the melting temperature of copper that you have found using this potential? |
</ | </ |
exercises/2015_ethz_mmm/t_melting.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1