Differences

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--- exercises:2018_ethz_mmm:h2o_md [2018/03/02 05:48] – dpasserone
+++ exercises:2018_ethz_mmm:h2o_md [2018/03/02 14:58] – dpasserone
@@ Line 9: / Line 9: @@
 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.
@@ Line 242: / Line 237: @@
   - Read the paper through section III to see which parameters are used for which interaction.
   - 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
-  - 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_displ.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>
+<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>