# Open SourceMolecular Dynamics

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exercises:2017_uzh_cmest:path_optimization_neb

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 exercises:2017_uzh_cmest:path_optimization_neb [2017/10/23 11:04]tmueller created exercises:2017_uzh_cmest:path_optimization_neb [2017/10/23 12:01]tmueller 2018/01/25 20:24 jglan 2017/10/23 12:01 tmueller 2017/10/23 11:04 tmueller created 2018/01/25 20:24 jglan 2017/10/23 12:01 tmueller 2017/10/23 11:04 tmueller created Last revision Both sides next revision Line 1: Line 1: ======= Path optimization using NEB ======= ======= Path optimization using NEB ======= - In the [[geometry_optimization|last ​exercise]] you have calculated the energy for Ethane for two slightly different geometries and noticed that the geometry optimization was not able to change one structure into the other with lower energy. As presented in the lecture, it may happen quiet often that a minimization algorithm gets stuck in a local minimum, respectively it is not guaranteed to find the global minimum. + In one of the [[geometry_optimization|last ​exercises]] you calculated the energy for Ethane for two slightly different geometries and noticed that the geometry optimization was not able to change one structure into the other with lower energy. As presented in the lecture, it may happen quiet often that a minimization algorithm gets stuck in a local minimum, respectively it is not guaranteed to find the global minimum. In this exercise, we will therefore perform Nudged Elastic Band (NEB) calculations using the same molecule as before and investigate the energy path between the two geometries. In this exercise, we will therefore perform Nudged Elastic Band (NEB) calculations using the same molecule as before and investigate the energy path between the two geometries. Line 158: Line 158: <​code>​ <​code>​ - $nohup mpirun -np 8 cp2k.popt -i ethane_neb_aba.inp -o ethane_neb_aba.out & +$ nohup mpirun -np 4 cp2k.popt -i ethane_neb_aba.inp -o ethane_neb_aba.out & ​ Line 173: Line 173: ​ - We replaced the CP2K executable ''​cp2k.sopt''​ with ''​cp2k.popt'',​ which is a parallel version of CP2K. By prefixing the command with ''​mpirun -np 8''​ we tell it to run it using the MPI system using 8 cores. And finally to have the command continue to run even if you log out, we prefixed everything with ''​nohup''​. The ampersand ''&''​ at the end is to run everything in the background. + We replaced the CP2K executable ''​cp2k.sopt''​ with ''​cp2k.popt'',​ which is a parallel version of CP2K. By prefixing the command with ''​mpirun -np 4''​ we tell it to run it using the MPI system using 4 cores. And finally to have the command continue to run even if you log out, we prefixed everything with ''​nohup''​. The ampersand ''&''​ at the end is to run everything in the background. This may take a couple of hours. Continue with the exercises below once the calculation finishes. This may take a couple of hours. Continue with the exercises below once the calculation finishes.