exercises:2016_ethz_mmm:t_melting
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exercises:2016_ethz_mmm:t_melting [2016/04/07 23:27] – yakutovich | exercises:2016_ethz_mmm:t_melting [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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* Download the 5.1 exercise into your $HOME folder and unzip it: | * Download the 5.1 exercise into your $HOME folder and unzip it: | ||
<code bash> | <code bash> | ||
- | you@eulerX ~$ wget http:// | + | you@eulerX ~$ wget http:// |
- | you@eulerX ~$ unzip exercises: | + | you@eulerX ~$ tar -zxvf exercises: |
you@eulerX ~$ cd exercise_5.1 | you@eulerX ~$ cd exercise_5.1 | ||
</ | </ | ||
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<note tip> | <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}} | + | All files of this exercise (**all inputs and scripts are commented**) can be also downloaded from the wiki: {{exercise_5.1.tar.gz|exercise_5.1.tar.gz}} |
</ | </ | ||
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* What is the physical meaning of the parameter ε in the Lennard-Jones potential? | * What is the physical meaning of the parameter ε in the Lennard-Jones potential? | ||
* What is the cohesive energy? How it can be related to the ε? Remember in the FCC structure one atom is surrounded by 12 neighbours. | * What is the cohesive energy? How it can be related to the ε? Remember in the FCC structure one atom is surrounded by 12 neighbours. | ||
- | * Melting temperature of Lennard-Jones system is about 1/12 of cohesive energy. Try to estimate it, because this estimation will be necessary | + | * Melting temperature of Lennard-Jones system is about 1/12 of cohesive energy. Try to estimate it, because this estimation will be used later |
</ | </ | ||
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<code bash> | <code bash> | ||
- | you@eulerX exercise_5.1$ cp2k.popt -i cell.inp -o cell.out | + | you@eulerX exercise_5.1$ |
</ | </ | ||
+ | |||
+ | <note tip> | ||
+ | * Repeat the simulation with a larger cutoff. How does the cohesive energy per atom change? Why? How does the equilibrium lattice parameter change? Why? | ||
+ | </ | ||
<note important> | <note important> | ||
- | Pay attention at the folowing | + | Pay attention at the following |
MULTIPLE_UNIT_CELL 4 2 2 | MULTIPLE_UNIT_CELL 4 2 2 | ||
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you@eulerX exercise_5.1$ tail -n 98 opt_cell-pos-1.xyz > ./ | you@eulerX exercise_5.1$ tail -n 98 opt_cell-pos-1.xyz > ./ | ||
</ | </ | ||
- | Among all the parameters that you should | + | For the next simulation |
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- | It is a 3000 step molecular dynamics. While it is running you can complete the first assignments. | + | It is a 10000 step molecular dynamics. While it is running you can complete the folowing |
<note tip> | <note tip> | ||
- Take a look at the file ELEMENT_opt_unit.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 ELEMENT_opt_unit.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. | ||
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</ | </ | ||
- | * 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. But again some parameters needs to be specified in the file nve.inp. Use the simulation cell from the file half-1.restart. Also file with coordinates (X_init_nve.xyz) needs to be created. Use the coordinates from the last frame of the previous run. | ||
+ | |||
+ | And run the simulations: | ||
<code bash> | <code bash> | ||
- | you@eulerX exercise_5.1$ bsub cp2k.popt -i 1400nve.inp -o 1400nve.out | + | you@eulerX exercise_5.1$ bsub cp2k.popt -i nve.inp -o nve.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 "nve-1.restart" |
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===== SIMULATIONS AT DIFFERENT TOTAL ENERGIES FOR DETERMINING THE MELTING TEMPERATURE ===== | ===== 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 " | + | As explained in the class, we should |
+ | in this case. | ||
**THE TEMPERATURE WILL NOT BE CONTROLLED DURING THE RUN** | **THE TEMPERATURE WILL NOT BE CONTROLLED DURING THE RUN** | ||
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- | * 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 TEMPnve.init.inp and TEMPnve.inp into 100nve.init.inp and 100nve.inp (for T=100) 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 | + | * Run the first simulation: bsub cp2k.popt -i 100nve.init.inp |
- | * Run the second simulation: bsub cp2k.popt -i 1300npe.inp > 1300npe.out | + | * Run the second simulation: bsub cp2k.popt -i 100nve.inp -o 100nve.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? | ||
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<note tip> | <note tip> | ||
- | * What is the melting temperature of copper | + | * What is the melting temperature of the noble gas that you have chosen? |
</ | </ |
exercises/2016_ethz_mmm/t_melting.1460071674.txt.gz · Last modified: 2020/08/21 10:15 (external edit)