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exercises:2015_uzh_molsim:cp2k [2015/05/04 22:47]
yakutovich
exercises:2015_uzh_molsim:cp2k [2015/05/04 23:57] (current)
yakutovich
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.txt · Last modified: 2015/05/04 23:57 by yakutovich