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--- exercises:2017_ethz_mmm:pythonmd [2017/03/03 05:26] – dpasserone
+++ exercises:2017_ethz_mmm:pythonmd [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== 38 atom Lennard-Jones cluster: molecular dynamics with python ======
+=====
+In this exercise you will perform molecular dynamics with a python program that you may inspect and modify directly. Then, you will perform the same kind of dynamics using cp2k and compare the performance. =====
+<note tip>
+All files of this exercise be downloaded from the wiki: {{e2_bis.zip|}}
+Download the exercise into your $HOME folder and unzip it.
+<code>
+you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:e2_bis.zip
+you@eulerX ~$ unzip exercises:2017_ethz_mmm:e2_bis.zip
+you@eulerX ~$ cd exercise_2
+</code>
+</note>
 <note tip>The instructions for loading the appropriate modules in .bashrc:
 <code>
@@ Line 21: / Line 37: @@
-In the repository you will find the program “**md.py**” and the geometry file “**fcc.xyz**”
+In the repository you will find the program “**md.py**” and the geometry file “**fcc_r.xyz**”
 The program md.py can perform a MD simulation for a system of Ar atoms interacting via Lennard-Jones potential.
@@ Line 59: / Line 75: @@
 <note warning>
-- Execute the program with input parameters:
+- **TASK 1** Execute the program with input parameters:
   * 0.5 as timestep
   * 1000 as total number of steps
@@ Line 67: / Line 83: @@
 Is the temperature of the system conserved?
-- Execute the program with input parameters
+- **TASK 2** Execute the program with input parameters
   * 1.8 as timestep
   * 1000 as total number of steps
@@ Line 96: / Line 112: @@
 prints=“False”</note>
 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 with 3-4 different timesteps.
+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?
 <note warning>
-- Initializing randomly the velocities of a finite system, the system will have a non zero total linear momentum and total angular momentum.
+- **TASK 3** Initializing randomly the velocities of a finite system, the system will have a non zero total linear momentum and total angular momentum.
 In the code we remove the total linear momentum after the initialization.
@@ Line 106: / Line 122: @@
 </note>
+----
+====== 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 (zip file) the input file **md.inp**, where the **&MOTION** section is different from the last lecture exercise.
+<code>
+&MOTION
+  &PRINT
+    &RESTART_HISTORY OFF
+    &END
+    &RESTART
+      &EACH
+        MD 5000
+      &END
+    &END
+    &TRAJECTORY
+      &EACH
+        MD 100
+      &END
+    &END
+  &END
+  &MD
+    ENSEMBLE NVE
+    STEPS 10000
+    TIMESTEP 0.5
+    TEMPERATURE 10.0
+  &END MD
+&END MOTION
+</code>
+<note important>
+- Run the code
+<code>
+> cp2k.popt -i md.inp > md.out
+</code>
+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:
+<code>python traj.py</code>
+</note>
+<note warning>Here an example of [[http://users.mccammon.ucsd.edu/~dzhang/energy-unit-conv-table.html|energy conversion table]]. </note>