exercises:2017_ethz_mmm:lennard_jones_cluster
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exercises:2017_ethz_mmm:lennard_jones_cluster [2017/02/23 16:37] – dpasserone | exercises:2017_ethz_mmm:lennard_jones_cluster [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== 38 atom Lennard-Jones cluster ====== | ====== 38 atom Lennard-Jones cluster ====== | ||
+ | |||
+ | {{: | ||
<note warning> | <note warning> | ||
TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
Line 31: | Line 33: | ||
<note tip> | <note tip> | ||
- | All files of this exercise | + | 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 | + | In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following |
- | {{ : | + | <note tip> |
+ | </ | ||
Login to euler using your nethz credentials. | Login to euler using your nethz credentials. | ||
- | Then go to the directory " | + | Then go to the directory " |
< | < | ||
- | you@eulerX ~$ cd exercise_1.1/38/ | + | you@eulerX ~$ cd exercise_1.1 |
+ | |||
</ | </ | ||
+ | |||
+ | ===== Geometry optimization | ||
+ | In this first part you will perform a simple energy optimization, | ||
+ | |||
The input file structure of the template is the following: | The input file structure of the template is the following: | ||
Line 151: | Line 159: | ||
| | ||
</ | </ | ||
+ | <note important> | ||
+ | **1 Hartree=27.2114 eV**. | ||
+ | In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in " | ||
+ | </ | ||
+ | <note tip> | ||
+ | - load the module with the special m_* bash functions and initialize the module: < | ||
+ | - randomize the coordinate files **fcc.xyz** | ||
+ | - 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 < | ||
+ | - run cp2k < | ||
+ | - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)** | ||
+ | - load vmd module 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. < | ||
+ | - plot q4 and energies with **gnuplot** (ask the teacher) | ||
+ | - 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: < | ||
+ | - finally, run the bash script < | ||
+ | </ | ||
- | <code bash c2h2.chain> | ||
- | |||
- | |||
- | |||
- | </ | ||
- | |||
- | |||
- | At this point submit the job grid, first loading the module for cp2k entering | ||
- | |||
- | < | ||
- | you@eulerX c2h2$ module load cp2k | ||
- | you@eulerX c2h2$ bsub cp2k.popt < c2h2.chain | ||
- | </ | ||
- | |||
- | |||
- | |||
- | |||
- | |||
- | < | ||
- | |||
- | </ | ||
- | |||
- | <code - fit.gnu> | ||
- | |||
- | </ | ||
- | |||
- | Compare the values that you obtain with the ones listed in the "human readable" | ||
- | |||
- | Now, perform the same exercise in another directory for the molecule C2H4. | ||
- | < | ||
- | you@eulerX c2h2$ cd ../c2h4 | ||
- | </ | ||
- | |||
- | |||
- | |||
- | <code coo.ch4> | ||
- | |||
- | </ | ||
- | |||
- | |||
- | <code bash c2h4.chain> | ||
- | |||
- | | ||
- | </ | ||
- | |||
- | | ||
<note tip> | <note tip> | ||
- | - Report the energy of the minimum | + | - Report the energy of the minima, compare it with the ones of the initial configurations. |
+ | - 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 | ||
- | - Plot the energy curve as a function | + | - Use " |
</ | </ |
exercises/2017_ethz_mmm/lennard_jones_cluster.1487867864.txt.gz · Last modified: 2020/08/21 10:15 (external edit)