exercises:2017_ethz_mmm:pythonmd
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| exercises:2017_ethz_mmm:pythonmd [2017/03/03 05:25] – dpasserone | exercises:2017_ethz_mmm:pythonmd [2017/03/03 05:50] – dpasserone | ||
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| + | ====== 38 atom Lennard-Jones cluster: molecular dynamics with python ====== | ||
| + | ===== | ||
| + | In this exercise you will perform molecular dynamics with a python program that you may inspect and modify directly. Then, you will perform the same kind of dynamics using cp2k and compare the performance. ===== | ||
| + | |||
| + | |||
| + | <note tip> | ||
| + | All files of this exercise be downloaded from the wiki: {{e2.zip|}} | ||
| + | Download the exercise into your $HOME folder and unzip it. | ||
| + | |||
| + | < | ||
| + | you@eulerX ~$ wget http:// | ||
| + | you@eulerX ~$ unzip exercises: | ||
| + | you@eulerX ~$ cd exercise_2 | ||
| + | </ | ||
| + | |||
| + | </ | ||
| <note tip>The instructions for loading the appropriate modules in .bashrc: | <note tip>The instructions for loading the appropriate modules in .bashrc: | ||
| Line 21: | Line 37: | ||
| - | In the repository you will find the program “**md.py**” and the geometry file “**fcc.xyz**” | + | In the repository you will find the program “**md.py**” and the geometry file “**fcc_r.xyz**” |
| The program md.py can perform a MD simulation for a system of Ar atoms interacting via Lennard-Jones potential. | The program md.py can perform a MD simulation for a system of Ar atoms interacting via Lennard-Jones potential. | ||
| Line 59: | Line 75: | ||
| <note warning> | <note warning> | ||
| - | - Execute the program with input parameters: | + | - **TASK 1** Execute the program with input parameters: |
| * 0.5 as timestep | * 0.5 as timestep | ||
| * 1000 as total number of steps | * 1000 as total number of steps | ||
| Line 67: | Line 83: | ||
| Is the temperature of the system conserved? | Is the temperature of the system conserved? | ||
| - | - Execute the program with input parameters | + | - **TASK 2** Execute the program with input parameters |
| * 1.8 as timestep | * 1.8 as timestep | ||
| * 1000 as total number of steps | * 1000 as total number of steps | ||
| Line 100: | Line 116: | ||
| <note warning> | <note warning> | ||
| - | - Initializing randomly the velocities of a finite system, the system will have a non zero total linear momentum and total angular momentum. | + | - **TASK 3** Initializing randomly the velocities of a finite system, the system will have a non zero total linear momentum and total angular momentum. |
| In the code we remove the total linear momentum after the initialization. | In the code we remove the total linear momentum after the initialization. | ||
| Find the section of the code that removes the initial linear momentum. What could you do to remove the initial angular momentum? (no need to write down the code, just think how you could do) | Find the section of the code that removes the initial linear momentum. What could you do to remove the initial angular momentum? (no need to write down the code, just think how you could do) | ||
| </ | </ | ||
| + | |||
| + | |||
| + | ---- | ||
| + | |||
| + | ====== Molecular dynamics using CP2K ====== | ||
| + | In this second part of the exercise, the same kind of dynamics will be performed with **cp2k**. You will find in the repository | ||
exercises/2017_ethz_mmm/pythonmd.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1