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--- exercises:2019_conexs_newcastle:ex3 [2019/09/10 12:33] – [MgS and MgO: Periodic systems and XAS] abussy
+++ exercises:2019_conexs_newcastle:ex3 [2019/09/10 16:43] – [MgO] abussy
@@ Line 2: / Line 2: @@
-In this exercise we are going to compute near-edge X-ray absorption spectra of bulk MgS and MgO, performing all-electron calculations with GAPW method, using the Transition Potential and $\Delta$SCF approaches. Our goal is to identify differences in the electronic structure, and as a consequence in the K-edge absorption spectrum, of the magnesium due to the different anions it os bounded to. We are also going to analyze the influence of basis set quality in the calculations.
+In this exercise we are going to compute near-edge X-ray absorption spectra of bulk MgS and MgO, performing all-electron calculations with GAPW method, using the Transition Potential and $\Delta$SCF approaches. Our goal is to identify differences in the electronic structure, and as a consequence in the K-edge absorption spectrum, of the magnesium due to the different anions it is bounded to. We are also going to analyze the influence of basis set quality in the calculations.
 Before starting, it is recommended to create one directory for each system (MgO and MgS) and, within the system's directory, create the subfolders 'optimization', 'dscf' and 'xas'.
@@ Line 103: / Line 103: @@
 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:
@@ Line 121: / Line 118: @@
 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>
@@ Line 379: / Line 376: @@
 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.