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--- exercises:2018_uzh_cmest:path_optimization_neb [2018/10/23 14:07] – [Path optimization using NEB] abussy
+++ exercises:2018_uzh_cmest:path_optimization_neb [2018/10/24 10:30] – [Vibrational analysis] abussy
@@ Line 173: / Line 173: @@
 </code>
-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. You can use the command "top" to check if there are enough cores available for your calculation.
+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 ?
-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.