exercises:2014_ethz_mmm:nudged_elastic_band
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exercise:nudged_elastic_band [2014/02/20 14:49] – oschuett | exercises:2014_ethz_mmm:nudged_elastic_band [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== Nudged Elastic Band ====== | ====== Nudged Elastic Band ====== | ||
- | 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.\\ | + | 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, |
- | 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 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 |
- | In 2D, there are at least two ways for doing so: \\ | + | |
- | A- Direct exchange with the central atom (PATH1): | + | In 2D, there are at least two ways for doing so: |
- | {{ : | + | |
- | B- Coordinated rotation of three atoms untill atom 2 is in the center(PATH2): | + | ^ Path 1 ^ Path 2 ^ |
- | {{ :exercise:neb_path2.gif |}} | + | | Direct exchange with the central atom | |
+ | | {{neb_path1.gif|}} | ||
- | ===== Path1: direct exchange ===== | ||
- | 1- Save the following commented CP2K input file to a file named '' | + | ===== Path 1: direct exchange ===== |
+ | |||
+ | === 1. Step === | ||
+ | Save the following commented CP2K input file to a file named '' | ||
| | ||
<code - neb1.inp> | <code - neb1.inp> | ||
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 115: | Line 121: | ||
&END FORCE_EVAL | &END FORCE_EVAL | ||
</ | </ | ||
- | + | === 2. Step: Run CP2K === | |
- | \\ | + | |
- | 2- Run CP2K | + | |
- | \\ | + | |
< | < | ||
$ cp2k.popt -i neb1.inp -o neb1.out | $ cp2k.popt -i neb1.inp -o neb1.out | ||
</ | </ | ||
- | 3- For the NEB calcualtions, | + | === 3. Step === |
+ | 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. | ||
- | 4- Checking the trajectory. \\ | + | === 4. Step: Checking the trajectory |
- | Here is a short script to create a '' | + | 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. | 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. | ||
< | < | ||
Line 136: | Line 140: | ||
</ | </ | ||
- | 5- Generating the energy profile. \\ | + | === 5. Step: Generating the energy profile |
- | 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 printed on screen. Any plotting program should be able to handle it. | ||
- | ===== Path2: Coordinated rotation ===== | + | The energy profile will be stored in the file '' |
+ | |||
+ | < | ||
+ | $ echo "plot ' | ||
+ | </ | ||
+ | |||
+ | ===== Path 2: Coordinated rotation ===== | ||
Here is the input file for the PATH2. | Here is the input file for the PATH2. | ||
Following the same procedure as above, you can obtain a trajectory and an energy profile. | Following the same procedure as above, you can obtain a trajectory and an energy profile. | ||
Line 170: | 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 210: | 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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1