exercises:2018_ethz_mmm:lennard_jones_cluster_2018
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exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/22 13:55] – dpasserone | exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:37] – dpasserone | ||
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+ | <note tip> | ||
+ | All files of this exercise be downloaded directly from the wiki: {{exercise_1.1.zip|}} | ||
+ | </ | ||
+ | |||
+ | Download the 1.1 exercise into your **EXERCISES** folder and unzip it. | ||
< | < | ||
- | max@qmobile: | + | max@qmobile: |
- | </ | + | max@qmobile: |
+ | max@qmobile: | ||
+ | max@qmobile: | ||
+ | </ | ||
- | Download the 1.1 exercise into your $HOME folder and unzip it. | ||
- | |||
- | < | ||
- | you@eulerX ~$ wget http:// | ||
- | you@eulerX ~$ unzip exercises: | ||
- | </ | ||
- | <!-- | ||
- | <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>{{ : | ||
</ | </ | ||
- | 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 tip> | <note tip> | ||
- | | + | - 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.< | + | - < |
- | python stein.py file.xyz </ | + | |
- 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)** | + | |
- | - load vmd module | + | - in the output file, grep the final energy |
+ | - 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. < | ||
- plot q4 and energies with **gnuplot** (ask the teacher) | - plot q4 and energies with **gnuplot** (ask the teacher) | ||
- 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 | ||
</ | </ | ||
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- Use " | - Use " | ||
</ | </ | ||
- | --> | + |
exercises/2018_ethz_mmm/lennard_jones_cluster_2018.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1