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--- exercises:2016_uzh_cmest:path_optimization_neb [2016/10/20 18:24] – [Visualize the trajectory] tmueller
+++ exercises:2016_uzh_cmest:path_optimization_neb [2016/10/20 19:30] – [Visualize the trajectory and plot the energy curve] tmueller
@@ Line 177: / Line 177: @@
 This may take a couple of hours. Continue with the exercises below once the calculation finishes.
-====== Visualize the trajectory ======
+====== Visualize the trajectory and plot the energy curve ======
 When you take another peek at the input file you used to run the calculation, you will notice that we specified ''NUMBER_OF_REPLICA 8'', which means that CP2K will generate in total 8 beads (3 we specified in the ''&REPLICA'' sections, 5 will be generated automatically by interpolation).
-You should therefore find 8 files named ''ethane_neb_aba-pos-Replica_nr_1-1.xyz''..''ethane_neb_aba-pos-Replica_nr_8-1.xyz'' in your exercise directory, containing the  optimization of each bead. To get the trajectory over the band, we extract the last frame (see the tip below) and write it into a separate file:
+You should therefore find 8 files named ''ethane_neb_aba-pos-Replica_nr_1-1.xyz''..''ethane_neb_aba-pos-Replica_nr_8-1.xyz'' in your exercise directory, containing the  optimization of each bead. To get the trajectory over the band, we extract the last frame (see the tip below) and write it into a separate file named ''ethane_neb_aba_8r.xyz'':
 <code>
@@ Line 214: / Line 214: @@
 </code>
 </note>
+Since CP2K writes the energy in the comment line of each frame in the XYZ file (see tip above), we can extract the energy values for each bead directly from the newly generated ''ethane_neb_aba_8r.xyz'':
+<code>
+awk '/E =/ {i=i+1; printf "%s %16.8f\n", i, $6}' ethane_neb_aba_8r.xyz
+</code>
+Create a plot for this energy curve.
+====== Vibrational analysis ======