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--- exercises:2018_ethz_mmm:infrared_2018 [2018/04/20 10:35] – dpasserone
+++ exercises:2018_ethz_mmm:infrared_2018 [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 11: / Line 11: @@
 ===== 1. Task: Computing vibrational spectra for methanol and benzene =====
 <code>
-$cp2k.sspm -i mdmet.inp > mdmet.out
+$cp2k.ssmp -i vibmet.inp > vibmet.out
+$cp2k.ssmp -i vibc6h6.inp > vibc6h6.out
 </code>
@@ Line 27: / Line 29: @@
 </code>
-<note warning>The ** .mol ** file for c6h6 is already there since the job is quite long (**C6H6-VIBRATIONS-1.ref.mol**)
+<note warning>The ** .mol ** file for c6h6 and methanol obtained with better precision (basis set) is already in the directory. (**C6H6-VIBRATIONS-1.ref.mol**) Using the command ** diff vib.c6h6.inp vib.c6h6.ref ** you can see the difference in the input parameters.
 </note>
@@ Line 48: / Line 50: @@
 </code>
-This code will generate frequencies and intensities of the IR spectrum in the files ** C6H6-VIBRATIONS.mol ** and ** MET-VIBRATIONS.mol **.
+This code will generate frequencies and intensities of the IR spectrum in the files ** C6H6-VIBRATIONS-1.mol ** and ** MET-VIBRATIONS-1.mol **.
 This file can be read by the visualization program **molden**.
 <note important>
-  * $ ./molden C6H6-VIBRATIONS-1.ref.mol
+  * $ ./molden C6H6-VIBRATIONS-1.mol
   * Use the "normal mode" check in the graphical interface. The spectrum appears.
   - Compare the one of methanol with experiments (see paper) and the one of benzene with literature on the internet.
   - Which kind of modes will correspond to stretching of CH and CC bonds?
   - Try to animate some frequencies, and report the kind of mode corresponding to all peaks.
+  - In the methanol case, you can compare the result you obtained with the one with better basis set and convergence.
+  - Examine the differences between the file vib.c6h6.inp and the vib.c6h6.ref, and the difference in spectra. Discuss.
 </note>
@@ Line 64: / Line 68: @@
 ===== 2. Task: Computing vibrational spectra using DFTB molecular dynamics =====
-You will find a fortran program in the repository, called ** dipole_correlation.f90 **
+You will find a fortran program in the repository, called ** dipole_correlation.f90 ** . This is already compiled and the executable is dipole.x.
-Compile it (module load gcc; gfortran -o dipole.x dipole_correlation.f90 ). This program computes the correlation function of the (derivative of) the dipole moment and performs the Fourier transform.
+ This program computes the correlation function of the (derivative of) the dipole moment and performs the Fourier transform.
+Run ** cp2k ** with the ** md*.inp ** input files (for the two molecules). Note that the dipole moment and derivatives are extracted from simulation and saved in a file dip*traj (check the input). Run first 5000 steps, then edit the file dipole.in  and run ** ./dipole.x < dipole.in **.
-Run ** cp2k ** with the ** md*.inp ** input files (for the two molecules). Note that the dipole moment and derivatives are extracted from simulation and saved in a file dip*traj (check the input). Run first 5000 steps, then edit the file dipole.in  and run ** dipole.x < dipole.in **.
 This will generate the autocorrelation function of the dipole derivative (why?) and its Fourier transform (frequency domain).
-<note important>  - Check the result. Is it satisfactory with respect to the DFT static calculation and literature? Why?
+<note important>  - Check the result. **gnuplot** with the command **plot "file" u 1:2 w l** will help. Is it satisfactory with respect to the DFT static calculation and literature? Why?
   - Run 40000 more steps. Check the new results. Discuss what you obtained. Discuss the behavior of the autocorrelation in the time domain.
+  - ** WEB SITE [[https://www.cfa.harvard.edu/hitran/vibrational.html|Vibrational modes]] **
 </note>