# Open SourceMolecular Dynamics

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exercises:2018_ethz_mmm:lennard_jones_cluster_2018

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 exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 03:15]dpasserone exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/04/14 14:50] (current)oschuett replace pdf with doi link Both sides previous revision Previous revision 2018/04/14 14:50 oschuett replace pdf with doi link2018/02/23 08:48 dpasserone 2018/02/23 08:37 dpasserone 2018/02/23 08:34 dpasserone 2018/02/23 08:34 dpasserone 2018/02/23 08:30 dpasserone 2018/02/23 08:24 dpasserone 2018/02/23 08:19 dpasserone 2018/02/23 03:43 dpasserone 2018/02/23 03:43 dpasserone 2018/02/23 03:32 dpasserone 2018/02/23 03:18 dpasserone 2018/02/23 03:17 dpasserone 2018/02/23 03:15 dpasserone 2018/02/22 17:00 dpasserone 2018/02/22 15:54 dpasserone 2018/02/22 15:52 dpasserone 2018/02/22 15:48 dpasserone 2018/02/22 14:33 dpasserone 2018/02/22 14:18 dpasserone 2018/02/22 13:55 dpasserone 2018/02/22 13:55 dpasserone created Next revision Previous revision 2018/04/14 14:50 oschuett replace pdf with doi link2018/02/23 08:48 dpasserone 2018/02/23 08:37 dpasserone 2018/02/23 08:34 dpasserone 2018/02/23 08:34 dpasserone 2018/02/23 08:30 dpasserone 2018/02/23 08:24 dpasserone 2018/02/23 08:19 dpasserone 2018/02/23 03:43 dpasserone 2018/02/23 03:43 dpasserone 2018/02/23 03:32 dpasserone 2018/02/23 03:18 dpasserone 2018/02/23 03:17 dpasserone 2018/02/23 03:15 dpasserone 2018/02/22 17:00 dpasserone 2018/02/22 15:54 dpasserone 2018/02/22 15:52 dpasserone 2018/02/22 15:48 dpasserone 2018/02/22 14:33 dpasserone 2018/02/22 14:18 dpasserone 2018/02/22 13:55 dpasserone 2018/02/22 13:55 dpasserone created Line 4: Line 4: - The command to run cp2k is the following: - + - max@qmobile:~$cp2k.ssmp -i file.inp -o file.out + All files of this exercise be downloaded directly from the wiki: {{exercise_1.1.zip|}} ​ - + - Download the 1.1 exercise into your$HOME folder and unzip it. + Download the 1.1 exercise into your **EXERCISES** ​folder and unzip it. <​code>​ <​code>​ + max@qmobile:​~$cd ; cd EXERCISES max@qmobile:​~$ wget http://​www.cp2k.org/​_media/​exercises:​2018_ethz_mmm:​exercise_1.1.zip max@qmobile:​~$wget http://​www.cp2k.org/​_media/​exercises:​2018_ethz_mmm:​exercise_1.1.zip max@qmobile:​~$ unzip exercises:​2018_ethz_mmm:​exercise_1.1.zip max@qmobile:​~$unzip exercises:​2018_ethz_mmm:​exercise_1.1.zip + max@qmobile:​~$ cd exercise_1.1 ​ - + - 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: - {{ :​exercises:​2017_ethz_mmm:​1999_the_double-funnel_energy_landscape_of_the_38-atom_lennard-jones_cluster.pdf |}} + [[doi>10.1063/​1.478595]] ​ - Login to euler using your nethz credentials. - Then go to the directory "​EXERCISES"​. ​ - <​code>​ - you@eulerX ~$cd exercise_1.1 + The command to run cp2k is the following (with a generic **file.inp** input file): + + <​code>​ + max@qmobile:​~$ cp2k.ssmp -i file.inp -o file.out +  ​ - ​ ===== Geometry optimization ​ ===== ===== Geometry optimization ​ ===== Line 147: Line 146: ​NOTE ON THE UNITS: CP2K USES SO CALLED "​atomic units"​. Meaning that the resulting energies are expressed in Hartree, ​ ​NOTE ON THE UNITS: CP2K USES SO CALLED "​atomic units"​. Meaning that the resulting energies are expressed in Hartree, ​ **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 "​temperature"​ units (there is a Boltzmann constant to make units work...). **The sigma value is in Angstrom.** + In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in "​temperature"​ units (there is a Boltzmann constant ​K_b to make units work...). ​<​code>​1 Kelvin*K_b=3.2E-6 Hartree​. Using this conversion factor you can transform the epsilon value into Hartree, and the total energy can be expressed in units of epsilon.  ​**The sigma value is in Angstrom.** - - randomize the coordinate files **fcc.xyz** ​ <​code>​m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz​Do the same with ico.xyz. You can look at all files with **vmd**. + - randomize the coordinate files **fcc.xyz** ​(which represents the "​cubic"​ structure) ​<​code>​m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz​Do the same with **ico.xyz** which represents the icosahedral structure. You can look at all files with **vmd**. - 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. - - <​code>​ python stein.py file.xyz ​You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**. ​ + - <​code>​ python stein.py file.xyz ​You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**. You will also be asked **"​value of l"** This means the symmetry of the order parameter, which is **l=4** in this case. - before running the simulation, copy the input coordinate file into in.xyz <​code>​cp fcc_rand.xyz in.xyz​ - before running the simulation, copy the input coordinate file into in.xyz <​code>​cp fcc_rand.xyz in.xyz​ - - run cp2k  <​code>​cp2k.ssmp -i geo_opt.inp -o geo_opt.out ​ + ​- 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. - - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)** + ​- run cp2k  <​code>​cp2k.ssmp -i geo_opt.inp ​| tee geo_opt.out ​ (to see the output on the screen as well), or **AS AN ALTERNATIVE** <​code>​cp2k.ssmp ​-i geo_opt.inp > geo_opt.out  ​(to retain the output in the geo_opt.out file only) + - in the output file, grep the final energy ​<​code>​grep "​ENERGY|“ geo_opt.out​ and transform it in the unit of the paper (epsilon units) - Open vmd and play with the optimization trajectory <​code>​vmd OPT-pos-1.xyz​ (ask the teacher) - Open vmd and play with the optimization trajectory <​code>​vmd OPT-pos-1.xyz​ (ask the teacher) - apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. <​code>​./​myq4 OPT-pos-1.xyz > fcc.ene.q4 ​ - apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. <​code>​./​myq4 OPT-pos-1.xyz > fcc.ene.q4 ​ Line 161: Line 161: - have a look at the myq4 script <​code>​nano myq4​ - have a look at the myq4 script <​code>​nano myq4​ - repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example: <​code>​mkdir FCC ; mv OPT* FCC ; mv geo_opt.out FCC​ - repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example: <​code>​mkdir FCC ; mv OPT* FCC ; mv geo_opt.out FCC​ - - finally, run the bash script <​code>​./​curve​. Look inside, and try to understand what you get. + - Run the bash script <​code>​./​curve​Look inside, and try to understand what you get. + - 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: ​Assignment: ​ ​Assignment: ​ - 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 "​epsilon"​ units, estimate the number of bonds in the cluster, assuming a pairwise interaction. - 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