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exercise:infra_red [2014/05/09 09:39] – dpasseroneexercises:2014_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 ======
-<note warning> 
-Credits for the nice programs of this lecture (correlation function + stm profile) are due to Leopold Talirz, Empa</note> 
  
 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 minima basis, but delivers nevertheless reasonable results due to an empirical correction term called //repulsion potential//.
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 <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 nodes with ''bsub -n 16'', particularly the vibrational spectrum. 
-Copy, as usual, the files from the directory **/cluster/home03/matl/danielep/LECTURE10/EXERCISE_10.1** (and later here on the media manager). +Download, as usual, the **commented** files from the wiki {{exercise_10.1.tar.gz|}}.
 </note> </note>
  
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 &END &END
 </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>
 +
 <note warning> <note warning>
 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!!
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 ===== Additional Files ===== ===== Additional Files =====
 Download the following file into your project directory: Download the following file into your project directory:
-  * {{:exercise:dftb_params.tgz|}}+  * {{dftb_params.tgz|}}
  
 You can unpack it with the following command: You can unpack it with the following command:
exercises/2014_ethz_mmm/infra_red.1399628385.txt.gz · Last modified: 2020/08/21 10:14 (external edit)