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exercises:2019_conexs_newcastle:ex3 [2019/09/10 12:34]
abussy [MgS and MgO: Periodic systems and XAS]
exercises:2019_conexs_newcastle:ex3 [2019/09/12 09:30]
abussy [Part 2: XAS calculations]
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 Do not forget to put in your work directory the files ''​GTH_POTENTIALS''​ and ''​GTH_BASIS_SETS'',​ which contain the parameters for the pseudopotentials and basis sets used in the calculations. Do not forget to put in your work directory the files ''​GTH_POTENTIALS''​ and ''​GTH_BASIS_SETS'',​ which contain the parameters for the pseudopotentials and basis sets used in the calculations.
  
-To run the calculation, type in your terminal:+To run the calculation ​follow the instructions on the page [[exercises:2019_conexs_newcastle:​ex0|Connecting to the HPC cluster]].
  
-<​code>​ 
-./cp2k.sopt -i MgO_opt.inp -o MgO_opt.out &  
-</​code> ​ 
  
 After the calculation is finished, you can check the files created in your directory. First open the output file ''​MgO_opt.out''​ and search for the following banner: ​ After the calculation is finished, you can check the files created in your directory. First open the output file ''​MgO_opt.out''​ and search for the following banner: ​
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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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 <note important>​Even though we are not changing the name of the basis set or pseupotential used, cp2k will use the parameters for the sulfur atom now, since the ''​ELEMENT''​ type is different. However, it is important to check in the ''​GTH_BASIS_SET''​ and ''​GTH_POTENTIALS''​ files whether the names are the same for different atoms.</​note>​ <note important>​Even though we are not changing the name of the basis set or pseupotential used, cp2k will use the parameters for the sulfur atom now, since the ''​ELEMENT''​ type is different. However, it is important to check in the ''​GTH_BASIS_SET''​ and ''​GTH_POTENTIALS''​ files whether the names are the same for different atoms.</​note>​
  
-Now the input is readyand can be run in the same way as before, just changing ​the input and output files names. +Now the input is ready and it can be run in the same way as before, just remember to change ​the file ''​cp2k.sh''​.
- +
-<​code>​ +
-./cp2k.sopt -i MgS_opt.inp -o MgS_opt.out &  +
-</​code> ​+
  
 After the calculation is finished, open the output file ''​MgS_opt.out''​ and look for the same banner as before. The optimized atomic positions are written in the file ''​MgS-pos-1.xyz''​. After the calculation is finished, open the output file ''​MgS_opt.out''​ and look for the same banner as before. The optimized atomic positions are written in the file ''​MgS-pos-1.xyz''​.
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   &DFT   &DFT
-    ​BASIS_SET_FILE_NAME ​ EMSL_BASIS_SETS ​basis set file with all-electron basis set +    !where to find all-electron basis sets and potentials 
-    POTENTIAL_FILE_NAME ​ POTENTIAL ​! file with parameters for all-electron calculations+    BASIS_SET_FILE_NAME ​ EMSL_BASIS_SETS 
 +    POTENTIAL_FILE_NAME ​ POTENTIAL ​
     UKS     UKS
  
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 <note important>​At this time we are using cartesian coordinates to indicate the position of the atoms, so the keyword ''​SCALED''​ should be removed.</​note>​ <note important>​At this time we are using cartesian coordinates to indicate the position of the atoms, so the keyword ''​SCALED''​ should be removed.</​note>​
  
-To run this calculation ​type in terminal: +To run this calculation ​proceed as you did before.
- +
-<​code>​ +
-./cp2k.sopt -i MgS_xas.inp -o MgS_xas.out & +
-</​code>​+
  
 This calculation should take longer than the geometry optimization to run. Once it is finished, check the number of warnings and if the calculation converged. Sometimes it does not converge within the maximum number of iterations we set in the input file. If this is the case, you can increase the number using the keyword ''​MAX_SCF''​. This calculation should take longer than the geometry optimization to run. Once it is finished, check the number of warnings and if the calculation converged. Sometimes it does not converge within the maximum number of iterations we set in the input file. If this is the case, you can increase the number using the keyword ''​MAX_SCF''​.
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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.
  
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 </​code>​ </​code>​
  
-For the MgS system, for example, run the calculation ​typing ​+instead of ''​TP_HH''​and you can run the calculation ​in the same way as you did before.
  
-<​code>​ +After the calculation ​is done, look for the message
-./cp2k.sopt -i MgS_dscf.inp -o MgS_dscf.out & +
-</​code>​ +
- +
-After the calculation ​ran, look for the message+
  
 <​code>​ <​code>​
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 <​note>​ In this exercise we have obtained absorption spectra using a simple basis set, in order to performed the calculations on small machines and using a limited time. Therefore, careful tests on basis set size, XC functional etc have to be carried out for production runs to get more reliable spectra. </​note> ​ <​note>​ In this exercise we have obtained absorption spectra using a simple basis set, in order to performed the calculations on small machines and using a limited time. Therefore, careful tests on basis set size, XC functional etc have to be carried out for production runs to get more reliable spectra. </​note> ​
  
 +
 +You can check the tutorial [[exercises:​2017_uzh_cp2k-tutorial:​gapw|Gaussian and Augmented Plane Wave Method]] in case you want to compute more absorption spectra.
  
  
  
exercises/2019_conexs_newcastle/ex3.txt · Last modified: 2019/09/13 10:57 by abussy