# Open SourceMolecular Dynamics

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exercises:2015_ethz_mmm:t_melting

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 exercises:2015_ethz_mmm:t_melting [2015/02/06 17:49]127.0.0.1 external edit exercises:2015_ethz_mmm:t_melting [2015/03/17 15:30] (current)yakutovich 2015/03/17 15:30 yakutovich 2015/03/17 13:42 yakutovich 2015/03/17 13:39 yakutovich 2015/03/17 12:51 yakutovich 2015/03/17 12:37 yakutovich 2015/03/17 12:19 yakutovich 2015/02/06 17:49 external edit Next revision Previous revision 2015/03/17 15:30 yakutovich 2015/03/17 13:42 yakutovich 2015/03/17 13:39 yakutovich 2015/03/17 12:51 yakutovich 2015/03/17 12:37 yakutovich 2015/03/17 12:19 yakutovich 2015/02/06 17:49 external edit Line 1: Line 1: ====== Determination of the melting temperature of copper ====== ====== Determination of the melting temperature of copper ====== + + + + 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 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: + - <​code>​ + - module load cp2k/trunk.2.5.13191 + * Download ​the 5.1 exercise into your $HOME folder and unzip it: - module load open_mpi/1.6.5 ! THIS IS NEEDED IF YOU WANT TO RUN AN MPI PARALLEL RUN --- NOT CONVENIENT IN THIS CASE + <​code ​bash> - module load vmd + you@eulerX ~$ wget http://www.cp2k.org/_media/​exercises:​2015_ethz_mmm:​exercise_5.1.zip - mkdir EX_5.1 + you@eulerX ~$unzip exercises:​2015_ethz_mmm:​exercise_5.1.zip - cd EX_5.1 + you@eulerX ~$ cd exercise_5.1 ​ - Copy into that directory the **COMMENTED** files that can be downloaded from the wiki: {{exercise_5.1.tar.gz|exercise_5.1.tar.gz}} ​ + + 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: - <​code>​ + <​code ​bash> - bsub cp2k.popt -i half.inp ​> half.out + you@eulerX exercise_5.1$​cp2k.popt -i half.inp ​-o half.out ​ - It is a 3000 step molecular dynamics. ​During this time (about 20 minutes) ​you can complete the first assignments. + It is a 3000 step molecular dynamics. ​While it is running ​you can complete the first assignments. - <​note ​important> + <​note ​tip> - ​* A1) Take a look at the file 111.xyz with vmd. Visualize it on the screen, and try to reproduce the figure similar to the one on the last slide of the lectures of today. Include the pbc box, create a representation with vdw, periodic images, rotate the sample, etc. Produce a snapshot and include the file in your assignment. + ​- Take a look at the file 111.xyz with vmd. Visualize it on the screen, and try to reproduce the figure similar to the one on the last slide of the lectures of today. Include the pbc box, create a representation with vdw, periodic images, rotate the sample, etc. Produce a snapshot and include the file in your assignment. - ​* A2) Take a look at the half.inp file. How is the temperature controlled? Are all particles moving? Why? Which are the relevant sections for MD? Which kind of MD is it? + ​- Take a look at the half.inp file. How is the temperature controlled? Are all particles moving? Why? Which are the relevant sections for MD? Which kind of MD is it? - ​* A3) Plot the -growing- half*ener file with gnuplot. How is temperature changing? Is there a conserved quantity? ​ + ​- Plot the -growing- half*ener file with gnuplot. How is temperature changing? Is there a conserved quantity? ​ ​ - At the end of the first dynamics (hint:** tail -f half*ener**) , you can examine the **half-pos-1.xyz** file by performing z-profiles using the script **doprof** ​. + * At the end of the first dynamics (hint:** tail -f half*ener**) , you can examine the **half-pos-1.xyz** file by performing z-profiles using the script **doprof**: - <​code>​ + <​code ​bash> - ./doprof half-pos-1.xyz ​ + you@eulerX exercise_5.1$ ​./doprof half-pos-1.xyz ​ ​ Line 39: Line 64: At the end, the file **movie.half-pos-1.xyz.gif**,​ an animated gif is produced. If it works, you can run the command: At the end, the file **movie.half-pos-1.xyz.gif**,​ an animated gif is produced. If it works, you can run the command: - <​code>​ + <​code ​bash> - animate -loop 0 -delay 100 movie.half-pos-1.xyz.gif ​ + you@eulerX exercise_5.1$​animate -loop 0 -delay 100 movie.half-pos-1.xyz.gif ​ ​ or download the file to your local machine and open in your internet browser. It will run the animation. ​ or download the file to your local machine and open in your internet browser. It will run the animation. ​ - <​note ​important> + <​note ​tip> - A4) Describe the profile you have obtained. What do you see? + ​- ​Describe the profile you have obtained. What do you see? ​ - Now, starting from the restart of this simulation, we equilibrate the system in nve, and we move all particles: + * Now, starting from the restart of this simulation, we equilibrate the system in nve, and we move all particles: - <​code>​ + <​code ​bash> - bsub cp2k.popt -i 1400nve.inp ​> 1400nve.out + you@eulerX exercise_5.1$ ​bsub cp2k.popt -i 1400nve.inp ​-o 1400nve.out ​ The resulting configuration (check) will be an equilibrated system (which profile?). The resulting configuration (check) will be an equilibrated system (which profile?). - Now we have a file called ​**1400nve-1.restart** + Now we have a file called ​"1400nve-1.restart"​. ​**Do not delete it !!!** It will be used as a restart file for all simulations. - **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 ===== Line 65: Line 90: 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). 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​ + **THE TEMPERATURE WILL NOT BE CONTROLLED DURING THE RUN** - For EACH temperature you have to: + For EACH temperature you should: - ​ + - * 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?​ How do you choose temperatures?​ * Observe the temperature and the z profile. Can you find the melting temperature?​ How do you choose temperatures?​ - ​ - - Note that you can run several A5-A7 steps at the same time and in the same directory.​ And finally... And finally... - <​note ​important> + <​note ​tip> - A8) WHAT IS THE MELTING TEMPERATURE OF THIS POTENTIAL (APPROXIMATELY)? + * What is the melting temperature of copper that you have found using this potential?