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--- exercises:2018_uzh_cmest:path_optimization_neb [2018/09/17 12:52] – external edit 127.0.0.1
+++ exercises:2018_uzh_cmest:path_optimization_neb [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 5: / Line 5: @@
 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.
-Following are three geometry files you should put/create in a new exercise directory:
+Following are four geometry files you should put/create in a new exercise directory:
 <code - ethane_1_opt.xyz>
@@ Line 173: / Line 173: @@
 </code>
-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.
+Note the use of ''mpirun -np 4'' together with the cp2k.popt executable. This tells the machine to run it using the MPI parallelization system on 4 cores, which should speed up your calculations. The prefix ''nohup'' lets the command continue even if you log out and the ampersand ''&'' makes it run in the background. Remember that tcopt2 is shared among you and that there is only a limited number of cores. Before launching, you can use the command ''top'' to check if there are enough cores available for your calculation.
 This may take a couple of hours. Continue with the exercises below once the calculation finishes.
@@ Line 300: / Line 300: @@
 </code>
-Once this run completes, you should find a file ''ethane_TS_va-VIBRATIONS-1.mol''.
+Once this run completes, you can grep for the modes frequency with:
-Now we are going to use the application //molden// (which you can load using ''module load molden'') to visualize the vibrational modes:
 <code>
-$ molden ethane_TS_va-VIBRATIONS-1.mol
+$ grep "VIB|Frequency" ethane_TS_va.out
 </code>
-Click the //Norm. Mode// checkbox in the //Molden Control// window to list all the modes. What is the lowest frequency you get? By clicking on it you can visualize it.
+The presence of a  negative (imaginary) mode means that it is actually a transition state (and not stable). Are there any of that kind for this structure ? If so, what are the atomic displacements associated with it ?
-The presence of a  negative (imaginary) mode means that it is actually a transition state (and not stable).
-Now repeat the same steps presented here for the bead with the lowest energy. What is now the first frequency you get in the list? Is this geometry stable?
-Please note: while you should get only 18 different frequencies you get 21 instead. That means that 3 frequencies are global rotations instead of modes in the molecule and should be ignored when looking for negative frequencies to identify whether a conformer is stable or not.
+Note that cp2k also produces a ''ethane_TS_va-VIBRATIONS-1.mol'' file. It is intended to be read by the ''Molden'' program, which makes the visualization of the modes possible.