exercises:2017_ethz_mmm:pythonmd
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exercises:2017_ethz_mmm:pythonmd [2017/03/03 05:50] – dpasserone | exercises:2017_ethz_mmm:pythonmd [2017/03/03 11:03] – dpasserone | ||
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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? | ||
Line 126: | Line 126: | ||
====== Molecular dynamics using CP2K ====== | ====== 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 | + | In this second part of the exercise, the same kind of dynamics will be performed with **cp2k**. You will find in the repository |
+ | < | ||
+ | &MOTION | ||
+ | |||
+ | & | ||
+ | &END | ||
+ | & | ||
+ | &EACH | ||
+ | MD 5000 | ||
+ | &END | ||
+ | &END | ||
+ | & | ||
+ | &EACH | ||
+ | MD 100 | ||
+ | &END | ||
+ | &END | ||
+ | &END | ||
+ | &MD | ||
+ | ENSEMBLE NVE | ||
+ | STEPS 10000 | ||
+ | TIMESTEP 0.5 | ||
+ | TEMPERATURE 10.0 | ||
+ | &END MD | ||
+ | &END MOTION | ||
+ | </ | ||
+ | |||
+ | <note important> | ||
+ | - Run the code | ||
+ | < | ||
+ | > cp2k.popt -i md.inp > md.out | ||
+ | </ | ||
+ | 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** | ||
+ | - 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? | ||
+ | - 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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1