exercises:2014_ethz_mmm:nudged_elastic_band
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exercise:nudged_elastic_band [2014/02/20 16:26] – sclelia | 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 | ||
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^ 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|}} |
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&END | &END | ||
& | & | ||
+ | & | ||
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3.8030201671 | 3.8030201671 | ||
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| | ||
| | ||
+ | & | ||
&END REPLICA | &END REPLICA | ||
& | & | ||
+ | & | ||
2.215467 | 2.215467 | ||
2.144383 | 2.144383 | ||
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| | ||
| | ||
+ | & | ||
&END REPLICA | &END REPLICA | ||
& | & | ||
+ | &COORD | ||
3.8030201671 | 3.8030201671 | ||
0.0000000000 | 0.0000000000 | ||
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| | ||
| | ||
- | | + | & |
+ | | ||
& | & | ||
&END MOTION | &END MOTION | ||
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& | & | ||
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 | ||
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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. | ||
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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 ===== | ||
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&END | &END | ||
&END | &END | ||
- | & | + | & |
+ | & | ||
-0.0000000000 | -0.0000000000 | ||
| | ||
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-1.9019119654 | -1.9019119654 | ||
-1.9019125593 | -1.9019125593 | ||
+ | & | ||
&END REPLICA | &END REPLICA | ||
- | & | + | & |
+ | & | ||
3.8030201671 | 3.8030201671 | ||
1.9019125593 | 1.9019125593 | ||
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+ | &END | ||
&END REPLICA | &END REPLICA | ||
- | & | + | & |
+ | & | ||
| | ||
0 0 0 | 0 0 0 | ||
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| | ||
-1.9019119654 | -1.9019119654 | ||
- | -1.9019125593 | + | -1.9019125593 |
+ | & | ||
&END REPLICA | &END REPLICA | ||
& | & | ||
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& | & | ||
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.1392913587.txt.gz · Last modified: 2020/08/21 10:14 (external edit)