# Open SourceMolecular Dynamics

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exercises:2015_ethz_mmm:t_melting

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 exercises:2015_ethz_mmm:t_melting [2015/03/17 12:19]yakutovich exercises:2015_ethz_mmm:t_melting [2015/03/17 15:30] (current)yakutovich Both sides previous 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 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 37: Line 37: - All files of this exercise (**all inputs are commented**) can be also downloaded from the wiki: {{exercise_5.1.zip|exercise_5.1.zip}} + 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: - you@eulerX exercise_5.1$​bsub cp2k.popt -i half.inp -o half.out + you@eulerX exercise_5.1$ 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> - 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. - 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? Line 82: Line 82: 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 90: 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: Line 99: Line 99: * 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... - * WHAT IS THE MELTING TEMPERATURE OF THIS POTENTIAL (APPROXIMATELY)? + * What is the melting temperature of copper that you have found using this potential?