# Open SourceMolecular Dynamics

### Site Tools

exercises:2017_ethz_mmm:geometry_optimization

# Differences

This shows you the differences between two versions of the page.

 — exercises:2017_ethz_mmm:geometry_optimization [2017/02/22 10:01] (current) Line 1: Line 1: + ====== 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''​ + + ​ + &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 + ​ + === 2. Step: Run CP2K === + <​code>​ + $cp2k.popt -i geopt.inp -o geopt.out + ​ + + === 3. Step === + For the GEO_OPT calculations,​ CP2k produces a few output files. The most important are: + + * geopt.out: standard CP2K output file. It tells you whether that the calculation is completed and what is the energy of the final configuration. + * geopt-pos-1.xyz : optimization trajectory. You can open it with VMD. + + === 4. Step: Checking the optimization trajectory === + <​code>​ +$ vmd  geopt-pos-1.xyz + ​ + + + 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 . + ​ + + === 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}' ​ + ​ + 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.