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.1392907758.txt.gz · Last modified: 2020/08/21 10:14 (external edit)