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exercises:2018_ethz_mmm:infrared_2018

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exercises:2018_ethz_mmm:infrared_2018 [2018/04/20 10:28] – created dpasseroneexercises:2018_ethz_mmm:infrared_2018 [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 <note tip> <note tip>
-You should run these calculations on 16 processors with ''bsub -n 16'', particularly the vibrational spectrum.  +You should run these calculations on your virtual machine. We will make severe approximation to fit this on your QM.  
-Download, as usual, the **commented** files from the wiki {{exercise-10.1.tar.gz|}}. +Download, as usual, the **commented** files from the wiki {{exercise_7.tgz|}}. 
-Please use command  **  tar xvf exercise-10.1.tar.gz  **  to extract files.+Please use command  **  tar xvzf exercise_7.tgz  **  to extract files.
 </note> </note>
  
 ===== 1. Task: Computing vibrational spectra for methanol and benzene ===== ===== 1. Task: Computing vibrational spectra for methanol and benzene =====
 <code> <code>
-$ bsub -n 2 mpirun cp2k.popt -i mdmet.inp -o mdmet.out+$cp2k.ssmp -i vibmet.inp > vibmet.out 
 +$cp2k.ssmp -i vibc6h6.inp > vibc6h6.out 
 </code> </code>
  
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 &VIBRATIONAL_ANALYSIS &VIBRATIONAL_ANALYSIS
  INTENSITIES  INTENSITIES
- NPROC_REP 16 
  DX 0.001  DX 0.001
    &PRINT    &PRINT
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 </code> </code>
  
-<note warning>The ** .mol ** file for c6h6 is already there since the job is quite long. However, if you plan to run it (maybe after the methanol case) remember to add the option to ask for more wallclock time ** -W HH:MM ** to bsub.+<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> </note>
  
-<note warning> +
-NPROC_REP has to be the same number of processors as in the bsub!! Edit the input!! +
-</note>+
  
 <code> <code>
-$ bsub -n 16 mpirun cp2k.popt -i vibmet.inp -o vibmet.out+./cp2k.ssmp -i vibmet.inp > vibmet.out
 </code> </code>
  
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 </code> </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**.  This file can be read by the visualization program **molden**. 
  
 <note important> <note important>
-  * $ module load courses mmm +   
-  * $ mmm-init  +  * $ ./molden C6H6-VIBRATIONS-1.mol
-  * $ molden C6H6-VIBRATIONS.mol+
   * Use the "normal mode" check in the graphical interface. The spectrum appears.   * 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.   - 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?   - 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.   - 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> </note>
-===== Additional Files ===== 
-Download the following file into your project directory: 
-  * {{dftb_params.tgz|}} 
  
-You can unpack it with the following command: +
-<code> +
-$ tar -xvzf dftb_params.tgz +
-</code>+
  
 ===== 2. Task: Computing vibrational spectra using DFTB molecular dynamics ===== ===== 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). 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.   - 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> </note>
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