exercises:2018_ethz_mmm:infrared_2018
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exercises:2018_ethz_mmm:infrared_2018 [2018/04/20 10:28] – created dpasserone | exercises: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 '' | + | 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 | + | Please use command |
</ | </ | ||
===== 1. Task: Computing vibrational spectra for methanol and benzene ===== | ===== 1. Task: Computing vibrational spectra for methanol and benzene ===== | ||
< | < | ||
- | $ bsub -n 2 mpirun | + | $cp2k.ssmp -i vibmet.inp > vibmet.out |
+ | $cp2k.ssmp | ||
</ | </ | ||
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& | & | ||
| | ||
- | | ||
DX 0.001 | DX 0.001 | ||
& | & | ||
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</ | </ | ||
- | <note warning> | + | <note warning> |
</ | </ | ||
- | <note warning> | + | |
- | NPROC_REP has to be the same number of processors as in the bsub!! Edit the input!! | + | |
- | </ | + | |
< | < | ||
- | $ bsub -n 16 mpirun | + | ./cp2k.ssmp -i vibmet.inp |
</ | </ | ||
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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> | ||
- | | + | |
- | * $ mmm-init | + | * $ ./molden C6H6-VIBRATIONS-1.mol |
- | * $ molden C6H6-VIBRATIONS.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, | ||
</ | </ | ||
- | ===== Additional Files ===== | ||
- | Download the following file into your project directory: | ||
- | * {{dftb_params.tgz|}} | ||
- | You can unpack it with the following command: | + | |
- | < | + | |
- | $ tar -xvzf dftb_params.tgz | + | |
- | </ | + | |
===== 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_2018.1524220110.txt.gz · Last modified: 2020/08/21 10:15 (external edit)