# CP2K Open Source Molecular Dynamics

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exercises:2017_ethz_mmm:geometry_optimization

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 exercises:2017_ethz_mmm:geometry_optimization [2017/02/22 10:01] exercises:2017_ethz_mmm:geometry_optimization [2020/08/21 10:15] (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 === + + $cp2k.popt -i geopt.inp -o geopt.out + + + === 3. Step === + For the GEO_OPT calculations, CP2k produces a few output files. The most important are: + + * geopt.out: standard CP2K output file. It tells you whether that the calculation is completed and what is the energy of the final configuration. + * geopt-pos-1.xyz : optimization trajectory. You can open it with VMD. + + === 4. Step: Checking the optimization trajectory === + +$ vmd  geopt-pos-1.xyz + + + + If VMD started up properly but the viewer window remains empty, try the following: + - 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: + + $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. 