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exercises:2019_conexs_newcastle:ex3 [2019/09/10 12:34] – [MgS and MgO: Periodic systems and XAS] abussyexercises:2019_conexs_newcastle:ex3 [2019/09/10 14:50] – [MgO] abussy
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 cp2k prints out the coordinates for each step of the calculation (they are indicated in the file by the index i, right below the number of atoms), so in order to use the optimized geometry in the following calculations, you should use the positions corresponding to the last iteration. cp2k prints out the coordinates for each step of the calculation (they are indicated in the file by the index i, right below the number of atoms), so in order to use the optimized geometry in the following calculations, you should use the positions corresponding to the last iteration.
  
-It is also important to check for warnings in your output file. In the end of the output file you can find the following banner:+It is also important to check for warnings in your output file. In the end of the file you can find the following banner:
  
 <code> <code>
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 As an output you are going to get two files: ''spectrum.inp'' and ''spectrum.out''. The first one contains the same information as the ''Mgs-xas_at1_st1.spectrum'' file, and in the second one you will find you absorption spectrum for atom 1. Change the name of the files to ''S_K-edge.inp'' and ''S_K-edge.out'', for example. You can now plot both absorption intensities from the file ''S_K-edge.inp'' and the convoluted spectrum from the file ''S_K-edge.out''. From the first one only the second and sixth columns need to be plotted.   As an output you are going to get two files: ''spectrum.inp'' and ''spectrum.out''. The first one contains the same information as the ''Mgs-xas_at1_st1.spectrum'' file, and in the second one you will find you absorption spectrum for atom 1. Change the name of the files to ''S_K-edge.inp'' and ''S_K-edge.out'', for example. You can now plot both absorption intensities from the file ''S_K-edge.inp'' and the convoluted spectrum from the file ''S_K-edge.out''. From the first one only the second and sixth columns need to be plotted.  
  
-In order to obtain the spectrum for atom 2, you can open the file ''get_average_spectrum.sh'', and replace ''at1'' by ''at2''in the line ''for i in $(ls ${DIR}/*xas_at2*spectrum)''. Run the script again and you will obtain the same two files again, but now with the absorption intensities and spectrum of atom 2. Change their names to ''Mg_K-edge.inp'' and ''Mg_K-edge.out'', and plot the +In order to obtain the spectrum for atom 2, you can open the file ''get_average_spectrum.sh'', and replace ''at1'' by ''at2'' in the line ''for i in $(ls ${DIR}/*xas_at2*spectrum)''. Run the script again and you will obtain the same two files again, but now with the absorption intensities and spectrum of atom 2. Change their names to ''Mg_K-edge.inp'' and ''Mg_K-edge.out'', and plot the 
 absorption spectrum. absorption spectrum.
  
exercises/2019_conexs_newcastle/ex3.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1