CP2K Open Source Molecular Dynamics

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====== Running a simple example with CP2K ======

For our computer experiments, we are going to use the [[http://cp2k.org|CP2K software]]. CP2K is under active development and some exercises require a recent CP2K version.

<code bash>
cp2k.sopt -h     # get version and revision number of your cp2k executable
</code>

CP2K does not have a graphical user interface, instead we use //input files// to tell CP2K what to do. 
Our input files have the file extension ''.in'' or ''.inp''. 

<note> **TASK 1**
  - Go to the directory ''intro/cp2k_first_run''
  - Run CP2K to perform a Molecular Dynamics of 32 water molecules. (Try different possibilities):
<code bash>
cp2k.sopt -i H2O-32.inp                   # run cp2k, writing output to screen
cp2k.sopt -i H2O-32.inp -o H2O-32.out     # run cp2k, writing output to file H2O-32.out
cp2k.sopt -i H2O-32.inp -o H2O-32.out  &  # as before, but run in background
</code>
</note>

<note tip>
To cancel running job simply use ''Ctrl''+''C''

If it runs in background use the following command:
<code bash>
killall -9 cp2k.sopt
</code>
</note>

<note> ** TASK 2**
While job is running open (use nano or vim) the input file 'H2O-32.inp' and try to get an overview of its structure.
</note>

CP2K creates several new files in the folder, most of which contain information on previous steps of the calculation (allowing e.g. to restart the calculation after a crash) and are not relevant at the moment. We are interested in the file H2O-32-pos-1.xyz, which contains the atomic positions during the steps of the Molecular Dynamics. Visualize the MD trajectory with VMD.

<code bash>
vmd H2O-32-pos-1.xyz
</code>

<note> **TASK 3**
  - Go to ''Graphics'' -> ''Representations...''. And change ''Drawing Method'' to **CPK**. 
  - Find the parameters of the periodic box in file H2O-32.inp  and draw it.
</note>

Now it's a right moment to 'play' a little bit with the input file. You can try the following things:
<note> **TASK 4**

  * Change the number of Molecular Dynamics (MD) steps. Check [[ http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/MOTION/MD.html#desc_STEPS  | MD section ]] in the manual
  * Instead of performing MD, make a single point calculation. Check [[ http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/GLOBAL.html#desc_RUN_TYPE  | RUN_TYPE ]] keyword in the manual
  * Change the DFT functional (instead of Pade use Blyp for example). Check [[ http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/DFT/XC/XC_FUNCTIONAL.html | in the manual]]
  * Change ensemble to NVT (needs additional [[ http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/MOTION/MD/THERMOSTAT.html | THERMOSTAT ]] section, ask assistant)
  * Make a geometry optimization (takes A LOT of time). Submit before you go home. 
</note>