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exercises:2017_ethz_mmm:geometry_optimization [2017/02/22 10:01] (current)
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 +====== Geometry Optimization ======
 +
 +In this exercise you will run a geometry optimization calculation,​ for two Kr atoms placed at distance $r=3.00Å$.
 +
 +=== 1. Step ===
 +Save the following commented CP2K input file to a file named ''​geopt.inp''​
 +
 +<code - 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 Kr Kr
 +          EPSILON ​   [K_e] 164.56
 +          SIGMA [angstrom] ​  3.601
 +          RCUT  [angstrom] ​ 25.0
 +        &END LENNARD-JONES
 +      &END NONBONDED
 +      &CHARGE
 +        ATOM Kr
 +        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
 +    Kr  0 0 0
 +    Kr  3 0 0
 +   &​END COORD
 +  &END SUBSYS
 +&END FORCE_EVAL
 +</​code>​
 +=== 2. Step: Run CP2K ===
 +<​code>​
 +$ cp2k.popt -i geopt.inp -o geopt.out
 +</​code>​
 +
 +=== 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 ===
 +<​code>​
 +$ vmd  geopt-pos-1.xyz
 +</​code>​
 +
 +<note tip>
 +If VMD started up properly but the viewer window remains empty, try the following:
 +  - Open the menu item //​Graphics//​ -> //​Representations...//​
 +  - In the appearing dialog set the //Drawing Methods// to //VDW// and the //Sphere Scale// to 0.2 .
 +</​note>​
 +
 +=== 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, until the minimum.
 +To check it, you can simply search the geopt.out file with the ''​grep''​ command:
 +<​code>​
 +$  grep ENERGY ​ geopt.out ​ | awk '​{print $9}' ​
 +</​code>​
 +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/2017_ethz_mmm/geometry_optimization.txt · Last modified: 2017/02/22 10:01 (external edit)