exercises:2018_ethz_mmm:lennard_jones_cluster_2018
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exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:34] – dpasserone | exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:48] – dpasserone | ||
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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> | ||
Line 153: | Line 153: | ||
- < | - < | ||
- before running the simulation, copy the input coordinate file into in.xyz < | - before running the simulation, copy the input coordinate file into in.xyz < | ||
+ | - Before running cp2k, check if the file **OPT-pos-1.xyz** is already present from a previous run. In that case remove or delete it accordingly. It contains the trajectory of the optimization. | ||
- run cp2k < | - run cp2k < | ||
- | - in the output file, grep the final energy < | + | - 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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<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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1