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exercises:2015_ethz_mmm:infra_red [2015/05/13 11:08] – [Infrared spectroscopy with molecular dynamics] pshindeexercises:2015_ethz_mmm:infra_red [2015/05/16 11:03] – pshinde
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 You should run these calculations on 16 nodes with ''bsub -n 16'', particularly the vibrational spectrum.  You should run these calculations on 16 nodes with ''bsub -n 16'', particularly the vibrational spectrum. 
 Download, as usual, the **commented** files from the wiki {{exercise-10.1.tar.gz|}}. Download, as usual, the **commented** files from the wiki {{exercise-10.1.tar.gz|}}.
 +Please use command  **  tar xvf exercise-10.1.tar.gz  **  to extract files.
 </note> </note>
  
 ===== 1. Task: Computing vibrational spectra for methanol and benzene ===== ===== 1. Task: Computing vibrational spectra for methanol and benzene =====
-To compute the vibrational spectra, we need to first find a minimum structure for the systems. To this end, we use the input files ** optc6h6.inp ** and **optmet.inp**. These runs are still done with DFT (not DFTB). The last geometry from the ** C6H6-pos.1.xyz ** is the optimized one. Copy it to optc6h6.xyz. This will be the input for the ** vibc6h6.inp ** which computes the spectra, by adding a new section in the input:+To compute the vibrational spectra, we need to first find a minimum energy structure for the systems. Here files optc6h6.xyz and optmet.xyz, present in exercise-10.1.tar.gz, are minimum energy structures. The geometry **optc6h6.xyz** will be the input for the **vibc6h6.inp** and **optmet.xyz** will be the input for the **vibmet.inp**. The following important section (present in the input files) computes the vibrational spectra.
  
 <code> <code>
 &VIBRATIONAL_ANALYSIS &VIBRATIONAL_ANALYSIS
  INTENSITIES  INTENSITIES
- NPROC_REP 32+ NPROC_REP 16
  DX 0.001  DX 0.001
    &PRINT    &PRINT
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 </code> </code>
  
-This code will generate frequencies and intensities of the IR spectrum in the files ** C6H6-VIBRATIONS.mol ** and the same for methanol. +This code will generate frequencies and intensities of the IR spectrum in the files ** C6H6-VIBRATIONS.mol ** and ** MET-VIBRATIONS.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 molden +  * $ module load courses mmm 
 +  * $ mmm-init 
   * $ molden C6H6-VIBRATIONS.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.
exercises/2015_ethz_mmm/infra_red.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1