exercises:2015_uzh_molsim:cp2k
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exercises:2015_uzh_molsim:cp2k [2015/05/04 12:07] – yakutovich | exercises:2015_uzh_molsim:cp2k [2015/05/04 23:57] – yakutovich | ||
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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 '' | + | Our input files have the file extension '' |
- | Many parameters are quite technical and not important at the moment, still it is very helpful to get an overview of the basic structure. | + | |
+ | < | ||
+ | - Go to the directory '' | ||
+ | - Run CP2K to perform a Molecular Dynamics of 32 water molecules. (Try different possibilities): | ||
+ | <code bash> | ||
+ | cp2k.sopt -i H2O-32.inp | ||
+ | cp2k.sopt -i H2O-32.inp -o H2O-32.out | ||
+ | cp2k.sopt -i H2O-32.inp -o H2O-32.out | ||
+ | </ | ||
+ | </ | ||
+ | <note tip> | ||
+ | To cancel running job simply use '' | ||
- | Run CP2K to perform a Molecular Dynamics of 32 water molecules. | + | If it runs in background use the following command: |
<code bash> | <code bash> | ||
- | cp2k.sopt | + | killall |
- | cp2k.sopt | + | |
- | cp2k.sopt -i H2O-32.inp -o H2O-32.out | + | |
</ | </ | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | While job is running open (use nano or vim) the input file ' | ||
+ | </ | ||
+ | |||
+ | 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, | ||
+ | |||
+ | <code bash> | ||
+ | vmd H2O-32-pos-1.xyz | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | - Go to '' | ||
+ | - Find the parameters of the periodic box in file H2O-32.inp | ||
+ | </ | ||
+ | |||
+ | Now it's a right moment to ' | ||
+ | < | ||
- | CP2K creates several new files in the folder, most of which contain information on previous | + | * Change |
+ | * Instead of performing MD, make a single point calculation. Check [[ http:// | ||
+ | * Change the DFT functional | ||
+ | * Change ensemble to NVT (needs additional [[ http:// | ||
+ | * Make a geometry optimization (takes A LOT of time). Submit before you go home. | ||
+ | </ |
exercises/2015_uzh_molsim/cp2k.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1