exercises:2018_ethz_mmm:lennard_jones_cluster_2018
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exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/22 17:00] โ dpasserone | exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2020/08/21 10:15] (current) โ external edit 127.0.0.1 | ||
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- | The command to run cp2k is the following: | ||
- | <code> | + | <note tip> |
- | max@qmobile:~$ cp2k.ssmp -i file.inp -o file.out | + | All files of this exercise be downloaded directly from the wiki: {{exercise_1.1.zip|}} |
- | </code> | + | </note> |
- | Download the 1.1 exercise into your $HOME folder and unzip it. | + | Download the 1.1 exercise into your **EXERCISES** |
< | < | ||
- | max@qmobile: | + | max@qmobile: |
+ | max@qmobile: | ||
max@qmobile: | max@qmobile: | ||
+ | max@qmobile: | ||
</ | </ | ||
- | <note tip> | + | |
- | All files of this exercise be downloaded from the wiki: {{exercise_1.1.zip|}} | + | |
- | </ | + | |
In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following paper about the energy landscape of the 38 atom Lennard-Jones cluster: | In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following paper about the energy landscape of the 38 atom Lennard-Jones cluster: | ||
- | <note tip>{{ : | + | <note tip>[[doi>10.1063/ |
</ | </ | ||
- | Login to euler using your nethz credentials. | ||
- | Then go to the directory " | ||
- | < | ||
- | you@eulerX ~$ cd exercise_1.1 | ||
+ | The command to run cp2k is the following (with a generic **file.inp** input file): | ||
+ | |||
+ | < | ||
+ | max@qmobile: | ||
+ | </ | ||
- | </ | ||
===== Geometry optimization | ===== Geometry optimization | ||
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<note important> | <note important> | ||
**1 Hartree=27.2114 eV**. | **1 Hartree=27.2114 eV**. | ||
- | In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in " | + | In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in " |
</ | </ | ||
<note tip> | <note tip> | ||
- | - randomize the coordinate files **fcc.xyz** | + | - randomize the coordinate files **fcc.xyz** |
- extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values. | - extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values. | ||
- | - < | + | - < |
- before running the simulation, copy the input coordinate file into in.xyz < | - before running the simulation, copy the input coordinate file into in.xyz < | ||
- | - run cp2k < | + | |
- | - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)** | + | |
+ | - in the output file, grep the final energy | ||
- Open vmd and play with the optimization trajectory < | - Open vmd and play with the optimization trajectory < | ||
- apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. < | - apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. < | ||
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- have a look at the myq4 script < | - have a look at the myq4 script < | ||
- repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example: < | - repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example: < | ||
- | - finally, run the bash script < | + | - Run the bash script < |
+ | - create a FCC_OUT subdirectory (**mkdir FCC_OUT ; cd FCC_OUT**) and copy there the files you want to keep; then go back one dir (**cd ..**), delete all the OPT* files (**rm OPT* **) and repeat the exercise with ico.xyz | ||
</ | </ | ||
Line 179: | Line 180: | ||
<note tip> | <note tip> | ||
- Report the energy of the minima, compare it with the ones of the initial configurations. | - Report the energy of the minima, compare it with the ones of the initial configurations. | ||
+ | - After converting the energy into " | ||
- Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Are the minima in two separate basins? | - Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Are the minima in two separate basins? | ||
- Report the value of the order parameter of the minumum, and discuss what you see | - Report the value of the order parameter of the minumum, and discuss what you see |
exercises/2018_ethz_mmm/lennard_jones_cluster_2018.1519318824.txt.gz ยท Last modified: 2020/08/21 10:15 (external edit)