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exercises:2016_ethz_mmm:infra_red [2016/02/03 09:54] – external edit 127.0.0.1exercises:2016_ethz_mmm:infra_red [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 ====== Infrared spectroscopy with molecular dynamics ====== ====== 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>10.1039/c3cp44302g]]. As in the last lectures, to make this exercise computationally feasible, we will use for MD the efficient Density Functional based Tight Binding (DFTB) method. It requires only a minima basis, but delivers nevertheless reasonable results due to an empirical correction term called //repulsion potential//.+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>10.1039/c3cp44302g]]. As in the last lectures, to make this exercise computationally feasible, we will use for MD the efficient Density Functional based Tight Binding (DFTB) method. It requires only a minimal basis but delivers nevertheless reasonable results due to an empirical correction term called //repulsion potential//.
  
 <note tip> <note tip>
-You should run these calculations on 16 nodes with ''bsub -n 16'', particularly the vibrational spectrum. +You should run these calculations on 16 processors 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. Please use command  **  tar xvf exercise-10.1.tar.gz  **  to extract files.
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 ===== 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 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> 
 +$ bsub -n 2 mpirun cp2k.popt -i mdmet.inp -o mdmet.out 
 +</code> 
 + 
 +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, contain minimum energy structures. 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>
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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 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> </note>
  
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 NPROC_REP has to be the same number of processors as in the bsub!! Edit the input!! NPROC_REP has to be the same number of processors as in the bsub!! Edit the input!!
 </note> </note>
-For the intensities, the derivative of the dipole along the normal modes is necessary (see lecture). So the moments are computed in the standard non periodic fashion:+ 
 +<code> 
 +$ bsub -n 16 mpirun cp2k.popt -i vibmet.inp -o vibmet.out 
 +</code> 
 + 
 +For the intensities, the derivative of the dipole along the normal modes is necessary (see lecture). So the moments are computed in the standard non-periodic fashion:
 <code> <code>
  &DFT  &DFT
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 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 ** 
-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 also the Fourier transform.+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  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 **.
exercises/2016_ethz_mmm/infra_red.1454493256.txt.gz · Last modified: 2020/08/21 10:15 (external edit)