exercises:2017_ethz_mmm:infra_red
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— | exercises:2017_ethz_mmm:infra_red [2020/08/21 10:15] (current) – created - external edit 127.0.0.1 | ||
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+ | ====== Infrared spectroscopy with molecular dynamics ====== | ||
+ | In this exercise, we will compare the vibrational spectrum of two molecules (methanol and benzene) computed with a static method (diagonalization of the dynamical matrix) and with molecular dynamics. The spectra for methanol are available in this paper [[doi> | ||
+ | |||
+ | <note tip> | ||
+ | You should run these calculations on 16 processors with '' | ||
+ | Download, as usual, the **commented** files from the wiki {{exercise-10.1.tar.gz|}}. | ||
+ | Please use command | ||
+ | </ | ||
+ | |||
+ | ===== 1. Task: Computing vibrational spectra for methanol and benzene ===== | ||
+ | < | ||
+ | $ bsub -n 2 mpirun cp2k.popt -i mdmet.inp -o mdmet.out | ||
+ | </ | ||
+ | |||
+ | To compute the vibrational spectra, we first need to find a minimum energy structure for the systems. The files optc6h6.xyz and optmet.xyz, present in exercise-10.1.tar.gz, | ||
+ | |||
+ | < | ||
+ | & | ||
+ | | ||
+ | | ||
+ | DX 0.001 | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | &END | ||
+ | </ | ||
+ | |||
+ | <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.popt -i vibmet.inp -o vibmet.out | ||
+ | </ | ||
+ | |||
+ | For the intensities, | ||
+ | < | ||
+ | & | ||
+ | BASIS_SET_FILE_NAME ./ | ||
+ | POTENTIAL_FILE_NAME ./ | ||
+ | |||
+ | & | ||
+ | | ||
+ | &END | ||
+ | &END | ||
+ | </ | ||
+ | |||
+ | 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**. | ||
+ | |||
+ | <note important> | ||
+ | * $ module load courses mmm | ||
+ | * $ mmm-init | ||
+ | * $ molden C6H6-VIBRATIONS.mol | ||
+ | * Use the " | ||
+ | - 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, | ||
+ | </ | ||
+ | ===== 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 ===== | ||
+ | |||
+ | You will find a fortran program in the repository, called ** dipole_correlation.f90 ** | ||
+ | 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. | ||
+ | |||
+ | 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). | ||
+ | |||
+ | <note important> | ||
+ | - Run 40000 more steps. Check the new results. Discuss what you obtained. Discuss the behavior of the autocorrelation in the time domain. | ||
+ | </ |
exercises/2017_ethz_mmm/infra_red.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1