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exercises:2015_ethz_mmm:geometry_optimization

Geometry Optimization

In this exercise you will run a geometry optimization calculation, for two Xe atoms placed at distance $r=3.00Å$.

1. Step

Save the following commented CP2K input file to a file named geopt.inp

geopt.inp
&GLOBAL
   RUN_TYPE GEO_OPT        
   PROJECT_NAME geopt  ! the calculation will produce a few output files, that will be labeled with this name
&END GLOBAL
&FORCE_EVAL
  METHOD FIST
  &MM
    &FORCEFIELD
        &SPLINE
          EMAX_SPLINE 10000    ! numeric parameter to ensure calculation stability. Should not be changed
        &END
        &NONBONDED
          &LENNARD-JONES
          atoms Xe Xe 
          EPSILON    [K_e] 232
          SIGMA [angstrom]   3.98
          RCUT  [angstrom]  25.0
        &END LENNARD-JONES
      &END NONBONDED
      &CHARGE
        ATOM Xe
        CHARGE 0.0
      &END CHARGE
    &END FORCEFIELD
    &POISSON
     PERIODIC NONE
      &EWALD
        EWALD_TYPE none
      &END EWALD
    &END POISSON
  &END MM
  &SUBSYS
   &CELL
    ABC [angstrom] 10 10 10
      PERIODIC NONE
   &END CELL
   &COORD
    UNIT angstrom
    Xe  0 0 0
    Xe  3 0 0
   &END COORD
  &END SUBSYS
&END FORCE_EVAL

2. Step: Run CP2K

$ cp2k.popt -i geopt.inp -o geopt.out

3. Step

For the GEO_OPT calculations, CP2k produces a few output files. The most important are:

  • geopt.out: standard CP2K output file. It tells you whether that the calculation is completed and what is the energy of the final configuration.
  • geopt-pos-1.xyz : optimization trajectory. You can open it with VMD.

4. Step: Checking the optimization trajectory

$ vmd  geopt-pos-1.xyz

If VMD started up properly but the viewer window remains empty, try the following:

  1. Open the menu item GraphicsRepresentations…
  2. In the appearing dialog set the Drawing Methods to VDW and the Sphere Scale to 0.2 .

5. Step: Checking the energy

In the geopt.out file you have a list of energies, one for each geometry optimization step that was performed. The overall energy should decrease, untill the minimum. To check it, you can simply search the geopt.out file with the grep command:

$  grep ENERGY  geopt.out  | awk '{print $9}' 

The energy at each step will be printed on screen.

6. Step

Run the input for different starting distances, and check whether the simulation always find the minimal energy configuration.

Questions

  • After running geometry optimization (on one set of parameters, starting from different distances), do you always find the minimum energy distance?
  • If not, report the distances at which the geometry optimization does not bring the system in the minimum energy configuration.
exercises/2015_ethz_mmm/geometry_optimization.txt · Last modified: 2015/02/18 15:46 by vondele