exercises:2017_ethz_mmm:pythonmd
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exercises:2017_ethz_mmm:pythonmd [2017/03/03 05:54] – dpasserone | exercises:2017_ethz_mmm:pythonmd [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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<note tip> | <note tip> | ||
- | All files of this exercise be downloaded from the wiki: {{e2.zip|}} | + | All files of this exercise be downloaded from the wiki: {{e2_bis.zip|}} |
Download the exercise into your $HOME folder and unzip it. | Download the exercise into your $HOME folder and unzip it. | ||
< | < | ||
- | you@eulerX ~$ wget http:// | + | you@eulerX ~$ wget http:// |
- | you@eulerX ~$ unzip exercises: | + | you@eulerX ~$ unzip exercises: |
you@eulerX ~$ cd exercise_2 | you@eulerX ~$ cd exercise_2 | ||
</ | </ | ||
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prints=“False”</ | prints=“False”</ | ||
execute three or four times the program and write down the execution time that you get as the only output. | execute three or four times the program and write down the execution time that you get as the only output. | ||
- | Now comment the lines for the “efficient” algorithm and uncomment the lines of the ”unefficient” one. Execute | + | Now comment the lines for the “efficient” algorithm and uncomment the lines of the ”unefficient” one. Execute 3-4 times. |
Is the execution time longer? Why do you think you get such a result? | Is the execution time longer? Why do you think you get such a result? | ||
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Compare the performance with the one of the python code. What do you notice? | Compare the performance with the one of the python code. What do you notice? | ||
Plot the energy by using the file **MD-1.ener** and **gnuplot** | Plot the energy by using the file **MD-1.ener** and **gnuplot** | ||
- | - What is the value of the total energy? Is it conserved? | + | |
- | - Increase the time step to 3 fs, and run it again. What happens to the total energy? | + | - Increase the time step to 3 fs, and run it again. What happens to the total energy? |
+ | - Note: to visualize a trajectory you can use the code (look inside it!) traj.py in the directory: | ||
+ | < | ||
</ | </ | ||
+ | |||
+ | <note warning> | ||
exercises/2017_ethz_mmm/pythonmd.1488520489.txt.gz · Last modified: 2020/08/21 10:15 (external edit)