exercises:2014_ethz_mmm:geometry_optimization
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+ | ====== Geometry Optimization ====== | ||
+ | |||
+ | In this exercise you will run a geometry optimization calculation, | ||
+ | |||
+ | === 1. Step === | ||
+ | Save the following commented CP2K input file to a file named '' | ||
+ | |||
+ | <code - geopt.inp> | ||
+ | &GLOBAL | ||
+ | | ||
+ | | ||
+ | &END GLOBAL | ||
+ | & | ||
+ | METHOD FIST | ||
+ | &MM | ||
+ | & | ||
+ | &SPLINE | ||
+ | EMAX_SPLINE 10000 ! numeric parameter to ensure calculation stability. Should not be changed | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | atoms Ar Ar | ||
+ | EPSILON | ||
+ | SIGMA [angstrom] | ||
+ | RCUT [angstrom] | ||
+ | &END LENNARD-JONES | ||
+ | &END NONBONDED | ||
+ | &CHARGE | ||
+ | ATOM Ar | ||
+ | CHARGE 0.0 | ||
+ | &END CHARGE | ||
+ | &END FORCEFIELD | ||
+ | & | ||
+ | | ||
+ | &EWALD | ||
+ | EWALD_TYPE none | ||
+ | &END EWALD | ||
+ | &END POISSON | ||
+ | &END MM | ||
+ | &SUBSYS | ||
+ | & | ||
+ | ABC [angstrom] 10 10 10 | ||
+ | PERIODIC NONE | ||
+ | & | ||
+ | & | ||
+ | UNIT angstrom | ||
+ | Ar 0 0 0 | ||
+ | Ar 2 0 0 | ||
+ | & | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | </ | ||
+ | === 2. Step: Run CP2K === | ||
+ | < | ||
+ | $ cp2k.popt -i geopt.inp -o geopt.out | ||
+ | </ | ||
+ | |||
+ | === 3. Step === | ||
+ | For the GEO_OPT calcualtions, | ||
+ | |||
+ | * 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 | ||
+ | </ | ||
+ | |||
+ | <note tip> | ||
+ | If VMD started up properly but the viewer window remains empty, try the following: | ||
+ | - Open the menu item // | ||
+ | - 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 ENERGY | ||
+ | </ | ||
+ | The energy at each step will be printed on screen. | ||
+ | |||
+ | === 6. Step === | ||
+ | Run the input for different satrting distances, and check whether the simulation always find the minimal energy configuration. To run multiple simulations, | ||