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exercises:2018_ethz_mmm:h2o_md [2018/03/02 11:01]
dpasserone
exercises:2018_ethz_mmm:h2o_md [2018/03/02 15:36] (current)
dpasserone
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 Download the 2.1 exercise into your **EXERCISES** folder and unzip it.  Download the 2.1 exercise into your **EXERCISES** folder and unzip it. 
  
-<​code>​ +
-max@qmobile:​~$ cd ; cd EXERCISES +
-max@qmobile:​~$ wget https://​polybox.ethz.ch/​index.php/​s/​ULaq6rjhg4Pu63A +
-max@qmobile:​~$ unzip exercise_2.1.zip +
-max@qmobile:​~$ cd exercise_2.1 +
-</​code>​+
  
 This exercise is mostly taken by a [[https://​www.cp2k.org/​exercises:​2015_uzh_molsim:​index|previous lab session]] by Marcella Iannuzzi, UZH, who should be credited and acknowledged here. This exercise is mostly taken by a [[https://​www.cp2k.org/​exercises:​2015_uzh_molsim:​index|previous lab session]] by Marcella Iannuzzi, UZH, who should be credited and acknowledged here.
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   - Run the **md300.in**:​ the command is <​code>​cp2k.ssmp -i md300.in > md300.out </​code>​   - Run the **md300.in**:​ the command is <​code>​cp2k.ssmp -i md300.in > md300.out </​code>​
   - Postprocess the trajectory to compute mean square displacement and velocity-velocity correlation function   - Postprocess the trajectory to compute mean square displacement and velocity-velocity correlation function
-  - Extract the diffusion coefficients and compare the two approaches:​ +  - Extract the diffusion coefficients and compare the two approaches ​(the instruction about the parameters**./​command.py -h**) 
-<​code>​vel_autocorr.py T300-vel-1.xyz 3 10 100  +<​code>​./vel_autocorr.py T300-vel-1.xyz 3 10 100  
-vel_autocorr_plot.py vel_autocorr.out +./vel_autocorr_plot.py vel_autocorr.out 
-mean_square_displ.py T300.xyz 3 10 100 +./​mean_square_disp.py T300.xyz 3 10 100 
-msd_fit_and_plot.py mean_square_disp.out+./msd_fit_and_plot.py mean_square_disp.out
 </​code>​ </​code>​
- +Remember: to display the **png** files, the command is <​code>​display file.png</​code>​ 
 +<note important>​Assignments 
 +  - look at the file T300-1.ener at the end of the simulation. It contains several quantities. Check the header! 
 +  - Using gnuplot, check the stability of the MD, you can also use <​code>​ ./​simpleplot.py Col1 Col2 </​code>​ 
 +  - How do you interpret the oscillation of the potential energy? And of temperature?​ 
 +  - Compare the values of the diffusion coefficient with the two methods. Are they compatible?  
 +  - Look at the trajectories with vmd. Why are the particles "​exiting"​ the box with time? What is the importance of this for the algorithm?​ 
 +  - Copy md300.in into md200.in and change the system name and the initial temperature. Run the md. What is the final temperature?​ Why? 
 +  - Copy md300.in into md400.in and change to 400 in the two places. Run the md. What is the final temperature?​ Why? 
 +  - Check the temperature dependence of the diffusion coefficient. Plot the result.
 </​note>​ </​note>​
  
  
exercises/2018_ethz_mmm/h2o_md.1519988490.txt.gz · Last modified: 2018/03/02 11:01 by dpasserone