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exercises:2017_ethz_mmm:geometry_optimization

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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)

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