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exercises:2018_ethz_mmm:h2o_md

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exercises:2018_ethz_mmm:h2o_md [2018/03/02 05:48] – dpasseroneexercises:2018_ethz_mmm:h2o_md [2020/08/21 10:15] (current) – external edit 127.0.0.1
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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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   - Read the paper through section III to see which parameters are used for which interaction.    - Read the paper through section III to see which parameters are used for which interaction. 
   - Recognize the parameters in the input file   - Recognize the parameters in the input file
-  - Run the **md300.in**: the command is <code>cp2k.ssmp -i md300.in > md300.out+  - 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>
  
  
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