exercises:2018_ethz_mmm:infrared_2018
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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 | ||
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===== 1. Task: Computing vibrational spectra for methanol and benzene ===== | ===== 1. Task: Computing vibrational spectra for methanol and benzene ===== | ||
< | < | ||
- | $cp2k.sspm -i mdmet.inp > mdmet.out | + | $cp2k.ssmp -i vibmet.inp > vibmet.out |
+ | $cp2k.ssmp -i vibc6h6.inp > vibc6h6.out | ||
</ | </ | ||
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- | <note warning> | + | <note warning> |
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- | 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> | ||
| | ||
- | * $ ./molden C6H6-VIBRATIONS-1.ref.mol | + | * $ ./molden C6H6-VIBRATIONS-1.mol |
* Use the " | * Use the " | ||
- 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, | - Try to animate some frequencies, | ||
+ | - 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, | ||
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===== 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 | + | 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 | ||
- | 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 | ||
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> | + | <note important> |
- 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:// | ||
</ | </ |
exercises/2018_ethz_mmm/infrared_2018.1524220502.txt.gz · Last modified: 2020/08/21 10:15 (external edit)