exercises:2016_ethz_mmm:nudged_elastic_band
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— | exercises:2016_ethz_mmm:nudged_elastic_band [2020/08/21 10:15] (current) – created - external edit 127.0.0.1 | ||
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+ | ====== Nudged Elastic Band ====== | ||
+ | In this exercise you will compute the energy profile for a simple reaction in a planar cluster of 7 Ar atoms with the NEB method. | ||
+ | |||
+ | The NEB method requires at least the start- and end-configuration between which the reaction path should be computed. In addition it is advantageous to add a guess for an intermediate configuration. This is useful in particular when multiple reaction paths are possible and one is interested in a specific one. By adding a suitable intermediate configuration, | ||
+ | |||
+ | The aim of this exercise is to compute the activation energy required for moving atom 2 (dark blue) into the center of the cluster. | ||
+ | |||
+ | In 2D there are at least two possible paths: | ||
+ | |||
+ | ^ Path 1 ^ Path 2 ^ | ||
+ | | Direct exchange with the central atom | Coordinated rotation of three atoms | | ||
+ | | {{neb_path1.gif|}} | ||
+ | |||
+ | |||
+ | ===== Path 1: direct exchange ===== | ||
+ | |||
+ | === 1. Step === | ||
+ | Save the following commented CP2K input file to a file named '' | ||
+ | | ||
+ | <code - neb1.inp> | ||
+ | &GLOBAL | ||
+ | | ||
+ | | ||
+ | &END GLOBAL | ||
+ | &MOTION | ||
+ | & | ||
+ | & | ||
+ | COMPONENTS_TO_FIX Z | ||
+ | LIST 1..7 | ||
+ | & | ||
+ | &END | ||
+ | &BAND | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | OPT_TYPE DIIS | ||
+ | &DIIS | ||
+ | | ||
+ | | ||
+ | &END | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | 3.8030201671 | ||
+ | | ||
+ | 1.9019125593 | ||
+ | 1.9019119654 | ||
+ | | ||
+ | | ||
+ | & | ||
+ | &END REPLICA | ||
+ | & | ||
+ | & | ||
+ | 2.215467 | ||
+ | 2.144383 | ||
+ | | ||
+ | 1.901913 | ||
+ | 1.901912 | ||
+ | | ||
+ | | ||
+ | & | ||
+ | &END REPLICA | ||
+ | & | ||
+ | &COORD | ||
+ | 3.8030201671 | ||
+ | 0.0000000000 | ||
+ | | ||
+ | 1.9019125593 | ||
+ | 1.9019119654 | ||
+ | | ||
+ | | ||
+ | & | ||
+ | &END REPLICA | ||
+ | & | ||
+ | &END MOTION | ||
+ | |||
+ | & | ||
+ | METHOD FIST | ||
+ | &MM | ||
+ | & | ||
+ | &SPLINE | ||
+ | EMAX_SPLINE 10000 | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | atoms Ar Ar | ||
+ | EPSILON | ||
+ | SIGMA [angstrom] | ||
+ | RCUT [angstrom] | ||
+ | &END LENNARD-JONES | ||
+ | &END NONBONDED | ||
+ | &CHARGE | ||
+ | ATOM Ar | ||
+ | CHARGE 0.0 | ||
+ | &END CHARGE | ||
+ | &END FORCEFIELD | ||
+ | & | ||
+ | PERIODIC NONE | ||
+ | &EWALD | ||
+ | EWALD_TYPE none | ||
+ | &END EWALD | ||
+ | &END POISSON | ||
+ | &END MM | ||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | ABC [angstrom] 20 20 20 | ||
+ | PERIODIC NONE | ||
+ | & | ||
+ | & | ||
+ | Ar -0.0000000000 | ||
+ | Ar | ||
+ | Ar -3.8030201671 | ||
+ | Ar | ||
+ | Ar | ||
+ | Ar -1.9019119654 | ||
+ | Ar -1.9019125593 | ||
+ | &END COORD | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | </ | ||
+ | === 2. Step: Run CP2K === | ||
+ | < | ||
+ | $ cp2k.popt -i neb1.inp -o neb1.out | ||
+ | </ | ||
+ | |||
+ | === 3. Step === | ||
+ | For the NEB calcualtions, | ||
+ | |||
+ | * neb1.out : standard CP2K output file. It tells you whether that the calculation is completed.\\ (See: | ||
+ | * neb1-pos-Replica_nr_XXX-1.xyz : those are the replica optimization trajectories. You get a trajectory for each replica. | ||
+ | * neb1-BANDXXX.out : geometry optimization output for each replica. | ||
+ | |||
+ | === 4. Step: Checking the trajectory === | ||
+ | Here is a short script to create a '' | ||
+ | Use this procedure to make sure that the trajectory you obtain is the one you actaully want to study. The movie.xyz can be read by VMD. | ||
+ | < | ||
+ | $ for a in 01 02 03 04 05 06 07 08 09 10 ; do tail -n 9 neb1-pos-Replica_nr_${a}-1.xyz >> movie.xyz ; done | ||
+ | </ | ||
+ | |||
+ | === 5. Step: Generating the energy profile === | ||
+ | |||
+ | Here is a short script to create an energy profile as a function of the replica number. | ||
+ | < | ||
+ | $ for a in 1 2 3 4 5 6 7 8 9 10 ; do grep ENERGY | ||
+ | </ | ||
+ | |||
+ | The energy profile will be stored in the file '' | ||
+ | |||
+ | < | ||
+ | $ echo "plot ' | ||
+ | </ | ||
+ | |||
+ | ===== Path 2: Coordinated rotation ===== | ||
+ | Here is the input file for the PATH2. | ||
+ | Following the same procedure as above, you can obtain a trajectory and an energy profile. | ||
+ | |||
+ | <code - neb2.inp> | ||
+ | &GLOBAL | ||
+ | | ||
+ | | ||
+ | &END GLOBAL | ||
+ | &MOTION | ||
+ | & | ||
+ | & | ||
+ | COMPONENTS_TO_FIX Z | ||
+ | LIST 1..7 | ||
+ | & | ||
+ | &END | ||
+ | &BAND | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | OPT_TYPE DIIS | ||
+ | &DIIS | ||
+ | | ||
+ | | ||
+ | &END | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | -0.0000000000 | ||
+ | | ||
+ | -3.8030201671 | ||
+ | | ||
+ | | ||
+ | -1.9019119654 | ||
+ | -1.9019125593 | ||
+ | & | ||
+ | &END REPLICA | ||
+ | & | ||
+ | & | ||
+ | 3.8030201671 | ||
+ | 1.9019125593 | ||
+ | | ||
+ | 0 0 0 | ||
+ | 1.9019119654 | ||
+ | | ||
+ | | ||
+ | &END | ||
+ | &END REPLICA | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | 0 0 0 | ||
+ | -3.8030201671 | ||
+ | | ||
+ | | ||
+ | -1.9019119654 | ||
+ | -1.9019125593 | ||
+ | & | ||
+ | &END REPLICA | ||
+ | & | ||
+ | &END MOTION | ||
+ | |||
+ | & | ||
+ | METHOD FIST | ||
+ | &MM | ||
+ | & | ||
+ | &SPLINE | ||
+ | EMAX_SPLINE 10000 | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | atoms Ar Ar | ||
+ | EPSILON | ||
+ | SIGMA [angstrom] | ||
+ | RCUT [angstrom] | ||
+ | &END LENNARD-JONES | ||
+ | &END NONBONDED | ||
+ | &CHARGE | ||
+ | ATOM Ar | ||
+ | CHARGE 0.0 | ||
+ | &END CHARGE | ||
+ | &END FORCEFIELD | ||
+ | & | ||
+ | PERIODIC NONE | ||
+ | &EWALD | ||
+ | EWALD_TYPE none | ||
+ | &END EWALD | ||
+ | &END POISSON | ||
+ | &END MM | ||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | ABC [angstrom] 20 20 20 | ||
+ | PERIODIC NONE | ||
+ | & | ||
+ | & | ||
+ | Ar -0.0000000000 | ||
+ | Ar | ||
+ | Ar -3.8030201671 | ||
+ | Ar | ||
+ | Ar | ||
+ | Ar -1.9019119654 | ||
+ | Ar -1.9019125593 | ||
+ | &END COORD | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | </ | ||
+ | |||
+ | ===== Questions ===== | ||
+ | * Sketch the reaction profile for the two paths presented, reporting shape and activation energy. | ||
+ | * What are the major differences between the profiles? How do you think the result will change by adopting different number of replicas? | ||