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exercises:2015_uzh_molsim:cp2k [2015/05/04 22:47]
yakutovich
exercises:2015_uzh_molsim:cp2k [2020/08/21 10:15] (current)
Line 8: Line 8:
  
 CP2K does not have a graphical user interface, instead we use //input files// to tell CP2K what to do.  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'' 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** 
-<tip+  - Go to the directory ''intro/cp2k_first_run'' 
-  -  +  Run CP2K to perform a Molecular Dynamics of 32 water molecules. (Try different possibilities):
-</tip> +
- +
-Run CP2K to perform a Molecular Dynamics of 32 water molecules.+
 <code bash> <code bash>
 cp2k.sopt -i H2O-32.inp                   # run cp2k, writing output to screen 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 gopt.out+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 cp2k.sopt -i H2O-32.inp -o H2O-32.out  &  # as before, but run in background
 </code> </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**
  
-CP2K creates several new files in the folder, most of which contain information on previous steps of the calculation (allowing e.gto restart the calculation after crashand 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 geometry optimization (takes A LOT of time). Submit before you go home.  
 +</note>
exercises/2015_uzh_molsim/cp2k.1430779636.txt.gz · Last modified: 2020/08/21 10:15 (external edit)