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exercises:2015_uzh_molsim:h2o_ff

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exercises:2015_uzh_molsim:h2o_ff [2015/04/23 12:20]
127.0.0.1 external edit
exercises:2015_uzh_molsim:h2o_ff [2020/08/21 10:15] (current)
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 We start with //ab initio// calculations that will form the basis for our fitting procedure. We start with //ab initio// calculations that will form the basis for our fitting procedure.
  
-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> +Have a look at cp2k input file. Can you guess what it does?
-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'' and below you see a commented example of such a file.  +
-Many parameters are quite technical and not important at the moment, still it is very helpful to get an overview of the basic structure +
- +
-Can you guess what it does?+
  
 <code bash gopt.in> <code bash gopt.in>
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 using density functional theory with the BLYP exchange-correlation functional. using density functional theory with the BLYP exchange-correlation functional.
  
 +Run CP2K to perform a geometry optimization of a water molecule.
  
-Run CP2K to find the optimal geometry of the water molecule. 
 <code bash> <code bash>
-cp2k.sopt -i gopt.in                # run cp2k, writing output to screen +cp2k.sopt -i gopt.in -o gopt.out 
-cp2k.sopt -i gopt.in -o gopt.out    # run cp2k, writing output to file gopt.out +
-cp2k.sopt -i gopt.in -o gopt.out &  # as before, but run in background+
 </code> </code>
  
-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 ''run-1H2O-GOPT-pos-1.xyz'', which contains the atomic positions during the steps of the geometry optimization. Visualize the optimized geometry with VMD. We are interested in the file ''run-1H2O-GOPT-pos-1.xyz'', which contains the atomic positions during the steps of the geometry optimization. Visualize the optimized geometry with VMD.
 <note>**TASK 2**  <note>**TASK 2** 
exercises/2015_uzh_molsim/h2o_ff.1429791640.txt.gz · Last modified: 2020/08/21 10:15 (external edit)