User Tools

Site Tools


exercises:2015_uzh_molsim:cp2k

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

exercises:2015_uzh_molsim:cp2k [2015/05/04 23:57]
yakutovich
exercises:2015_uzh_molsim:cp2k [2020/08/21 10:15]
Line 1: Line 1:
-====== 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> 
exercises/2015_uzh_molsim/cp2k.txt ยท Last modified: 2020/08/21 10:15 (external edit)