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--- exercises:2015_uzh_molsim:cp2k [2015/05/04 12:07] – yakutovich
+++ exercises:2015_uzh_molsim:cp2k [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 8: / Line 8: @@
 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'' and below you see a commented example of such a file.
+Our input files have the file extension ''.in'' or ''.inp''.
-Many parameters are quite technical and not important at the moment, still it is very helpful to get an overview of the basic structure.
+<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''
-Run CP2K to perform a Molecular Dynamics of 32 water molecules.
+If it runs in background use the following command:
 <code bash>
-cp2k.sopt -i H2O-32.inp                      # run cp2k, writing output to screen
+killall -9 cp2k.sopt
-cp2k.sopt -i H2O-32.inp -o H2O-32.out     # run cp2k, writing output to file gopt.out
-cp2k.sopt -i H2O-32.inp -o H2O-32.out  &  # as before, but run in background
 </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**
-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.
+  * 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>