exercises:2014_ethz_mmm:nudged_elastic_band
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| exercise:nudged_elastic_band [2014/02/20 15:21] – oschuett | exercises:2014_ethz_mmm:nudged_elastic_band [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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| In this exercise you will compute the energy profile for a simple reaction in a planar cluster of 7 Ar atoms, by using the NEB method. | In this exercise you will compute the energy profile for a simple reaction in a planar cluster of 7 Ar atoms, by using the NEB method. | ||
| - | The NEB method requires at least the starting and the ending configuration between which the path is to be computed. In addition is good to add a guess of the intermediate configuration. This is useful in particular when two or more three reaction paths are possible and you want to compute the activation energy of a determined path. By adding the desired intermediate configuration, | + | The NEB method requires at least the starting and the ending configuration between which the path is to be computed. In addition is good to add a guess of the intermediate configuration. This is useful in particular when two or more reaction paths are possible and you want to compute the activation energy of a determined path. By adding the desired intermediate configuration, |
| The aim of this exercise is to compute the activation energy required for bringing | The aim of this exercise is to compute the activation energy required for bringing | ||
| Line 10: | Line 10: | ||
| ^ Path 1 ^ Path 2 ^ | ^ Path 1 ^ Path 2 ^ | ||
| | Direct exchange with the central atom | Coordinated rotation of three atoms | | | Direct exchange with the central atom | Coordinated rotation of three atoms | | ||
| - | | {{:exercise:neb_path1.gif|}} | + | | {{neb_path1.gif|}} |
| Line 42: | Line 42: | ||
| &END | &END | ||
| & | & | ||
| - | Ar | + | & |
| - | | + | -0.0000000000 |
| - | | + | 3.8030201671 |
| - | | + | |
| - | | + | 1.9019125593 |
| - | | + | 1.9019119654 |
| - | | + | |
| + | | ||
| + | & | ||
| &END REPLICA | &END REPLICA | ||
| & | & | ||
| - | Ar 2.215467 | + | & |
| - | | + | |
| - | | + | 2.144383 |
| - | | + | |
| - | | + | 1.901913 |
| - | | + | 1.901912 |
| - | | + | |
| + | | ||
| + | & | ||
| &END REPLICA | &END REPLICA | ||
| & | & | ||
| - | | + | |
| - | | + | |
| - | | + | 0.0000000000 |
| - | | + | |
| - | | + | 1.9019125593 |
| - | | + | 1.9019119654 |
| - | | + | |
| - | &END REPLICA | + | |
| + | & | ||
| + | &END REPLICA | ||
| & | & | ||
| &END MOTION | &END MOTION | ||
| Line 81: | Line 87: | ||
| & | & | ||
| atoms Ar Ar | atoms Ar Ar | ||
| - | EPSILON 119.8 | + | EPSILON |
| - | SIGMA 3.401 | + | SIGMA [angstrom] |
| - | RCUT 25.0 | + | RCUT |
| &END LENNARD-JONES | &END LENNARD-JONES | ||
| &END NONBONDED | &END NONBONDED | ||
| Line 123: | Line 129: | ||
| For the NEB calcualtions, | For the NEB calcualtions, | ||
| - | * neb1.out : standard CP2K output file. It tells you whether that the calculation is completed. (See:[[exercise:single_point_calculation|Computation of the Lennard Jones curve for two Ar atoms]].Part I, Step 3) | + | * 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-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. | * neb1-BANDXXX.out : geometry optimization output for each replica. | ||
| Line 138: | Line 144: | ||
| Here is a short script to create an energy profile as a function of the replica number. | 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 | + | $ 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 ' | ||
| </ | </ | ||
| - | The energy profile will be printed on screen. Any plotting program should be able to handle it. | ||
| ===== Path 2: Coordinated rotation ===== | ===== Path 2: Coordinated rotation ===== | ||
| Line 169: | Line 180: | ||
| &END | &END | ||
| &END | &END | ||
| - | & | + | & |
| - | Ar | + | & |
| - | Ar 3.8030201671 | + | -0.0000000000 |
| - | Ar | + | |
| - | Ar 1.9019125593 | + | -3.8030201671 |
| - | Ar 1.9019119654 | + | |
| - | Ar | + | |
| - | Ar | + | -1.9019119654 |
| + | -1.9019125593 | ||
| + | & | ||
| &END REPLICA | &END REPLICA | ||
| - | & | + | & |
| - | Ar | + | & |
| - | Ar | + | 3.8030201671 |
| - | Ar -3.8030201671 | + | 1.9019125593 |
| - | Ar 0 0 0 | + | |
| - | Ar | + | 0 0 0 |
| - | Ar -1.9019119654 | + | 1.9019119654 |
| - | Ar -1.9019125593 | + | |
| + | | ||
| + | &END | ||
| &END REPLICA | &END REPLICA | ||
| - | & | + | & |
| - | Ar 1.9019125593 | + | & |
| - | Ar 0 0 0 | + | 1.9019125593 |
| - | Ar | + | 0 0 0 |
| - | Ar 3.8030201671 | + | -3.8030201671 |
| - | Ar 1.9019119654 | + | |
| - | Ar | + | |
| - | Ar | + | -1.9019119654 |
| + | -1.9019125593 | ||
| + | & | ||
| &END REPLICA | &END REPLICA | ||
| & | & | ||
| Line 209: | Line 226: | ||
| & | & | ||
| atoms Ar Ar | atoms Ar Ar | ||
| - | EPSILON 119.8 | + | EPSILON |
| - | SIGMA 3.401 | + | SIGMA [angstrom] |
| - | RCUT 25.0 | + | RCUT |
| &END LENNARD-JONES | &END LENNARD-JONES | ||
| &END NONBONDED | &END NONBONDED | ||
exercises/2014_ethz_mmm/nudged_elastic_band.1392909660.txt.gz · Last modified: 2020/08/21 10:14 (external edit)