XANES in Diamond - Revision history

Karsai: /* Step 4 Extraction of XAS Spectrum */

2022-04-15T15:30:24Z

Step 4 Extraction of XAS Spectrum

← Older revision		Revision as of 15:30, 15 April 2022
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	<div class="toccolours mw-customtoggle-script">'''Click to show/''gnuplot_XANES_C.script''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show/''gnuplot_XANES_C.script''</div>
	<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:~~gnuplot_XANES_C}}~~</div>		<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">
			<pre>
			unset ytics
			set xrange [280:310]
			set xlabel "Energy (eV)"
			set ylabel "Absorption (arbitrary units)"
			plot "CORE_DIELECTRIC_IMAG.dat" using 1:2 with lines lw 2 ti "VASP",\
			"C_PARATEC_aligned_to_VASP.dat" using 1:2 with lines ti "PAW lit",\
			"C_XAS_aligned_to_VASP.dat" using 1:2 with lines ti "Exp"
			pause -1
			</pre>
			</div>

	To use that script type:		To use that script type:

Karsai: /* Step 4 Extraction of XAS Spectrum */

2022-04-15T15:24:23Z

Step 4 Extraction of XAS Spectrum

@@ Line 119: / Line 119: @@
 <div class="toccolours mw-customtoggle-script">'''Click to show/''plot_core_imdiel.sh''</div>
-<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:plot_core_imdiel}}</div>
+<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">
 To use it type:

Karsai: /* Step 4 Extraction of XAS Spectrum */

2021-12-27T09:09:28Z

Step 4 Extraction of XAS Spectrum

← Older revision		Revision as of 09:09, 27 December 2021
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	Because DFT cannot reproduce the absolute position (see above), we have shifted both spectra so that the position of the first peak coincides with the VASP. In this example, we scaled the experiment to VASP, since in this way the obtained results can be very easily compared using a script. Usually one would either scale the first peak to 0 or would scale the calculated value to the experiment. Additionally the intensity of the spectrum can be scaled arbitrarily. So in this example, we align the position and the height of the first peak for the calculations. The experiment is a little bit more tricky. It's a matter of taste what to consider as the first peak, but we decided that most likely the second peak corresponds to the first peak in the calculations and the first peak in experiment is a shoulder that is simply not pronounced in the calculations.		Because DFT cannot reproduce the absolute position (see above), we have shifted both spectra so that the position of the first peak coincides with the VASP. In this example, we scaled the experiment to VASP, since in this way the obtained results can be very easily compared using a script. Usually one would either scale the first peak to 0 or would scale the calculated value to the experiment. Additionally the intensity of the spectrum can be scaled arbitrarily. So in this example, we align the position and the height of the first peak for the calculations. The experiment is a little bit more tricky. It's a matter of taste what to consider as the first peak, but we decided that most likely the second peak corresponds to the first peak in the calculations and the first peak in experiment is a shoulder that is simply not pronounced in the calculations.

	Another important issue is the broadening. Because the observed broadening is driven by many factors depending on the particular experimental setup, it is not possible to reproduce the broadening exactly. Therefore, we arbitrarily choose a broadening that gives approximately the same width as experiment. For simplicity in this tutorial, we choose to use a 0.5 eV constant ~~Lorentzian~~ broadening (~~this~~ is the ~~only type of~~ broadening ~~built in for the calculation of XAS spectra in VASP~~). For more elaborate spectra we strongly advise users to choose a 0.05 eV broadening and apply the desired broadening as post-processing.		Another important issue is the broadening. Because the observed broadening is driven by many factors depending on the particular experimental setup, it is not possible to reproduce the broadening exactly. Therefore, we arbitrarily choose a broadening that gives approximately the same width as experiment. For simplicity in this tutorial, we choose to use a 0.5 eV constant Gaussian broadening (the broadening is determined by the {{TAG\|ISMEAR}} tag and we used {{TAG\|ISMEAR}}=0 which corresponds to a Gaussian broadening). For more elaborate spectra we strongly advise users to choose a 0.05 eV broadening and apply the desired broadening as post-processing.

	Apart from the lower broadening width, we get a quite reasonable agreement with the theoretical literature calculation. We stress again that the <math>3\times3\times3</math> super cell in this example are not fully converged. The interested user can repeat the calculations for a larger <math>4\times4\times4</math> super cell. The files for this example are also given in the tar file. Be aware that the larger number of atoms in the bigger super cell requires an adjustment of the {{TAG\|NBANDS}} variable..		Apart from the lower broadening width, we get a quite reasonable agreement with the theoretical literature calculation. We stress again that the <math>3\times3\times3</math> super cell in this example are not fully converged. The interested user can repeat the calculations for a larger <math>4\times4\times4</math> super cell. The files for this example are also given in the tar file. Be aware that the larger number of atoms in the bigger super cell requires an adjustment of the {{TAG\|NBANDS}} variable..

Karsai: /* Step 4 Extraction of XAS Spectrum */

2021-07-19T08:24:26Z

Step 4 Extraction of XAS Spectrum

← Older revision		Revision as of 08:24, 19 July 2021
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	=== Step 4 Extraction of XAS Spectrum ===		=== Step 4 Extraction of XAS Spectrum ===

	The XAS spectrum is the imaginary part of the frequency-dependent dielectric function, which is written in the {{TAG\|OUTCAR}} file		The XAS spectrum is proportional to the imaginary part of the frequency-dependent dielectric function, which is written in the {{TAG\|OUTCAR}} file
	frequency dependent IMAGINARY DIELECTRIC FUNCTION (independent particle, no local field effects) density-density		frequency dependent IMAGINARY DIELECTRIC FUNCTION (independent particle, no local field effects) density-density
	E(ev) X Y Z XY YZ ZX		E(ev) X Y Z XY YZ ZX

Karsai: /* Step 4 Extraction of XAS Spectrum */

2020-09-02T15:08:34Z

Step 4 Extraction of XAS Spectrum

← Older revision		Revision as of 15:08, 2 September 2020
Line 116:		Line 116:
	...		...

	Usually we are interested in the sum of all components of the dielectric matrix. You can obtain this by the script provided in this tutorial ''plot_core_imdiel.pl''		Usually we are interested in the sum of all components of the dielectric matrix. You can obtain this by the script provided in this tutorial ''plot_core_imdiel.sh''

	<div class="toccolours mw-customtoggle-script">'''Click to show/''plot_core_imdiel.pl''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show/''plot_core_imdiel.sh''</div>
	<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:plot_core_imdiel}}</div>		<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:plot_core_imdiel}}</div>

	To use it type:		To use it type:
	bash ./plot_core_imdiel.pl		bash ./plot_core_imdiel.sh

	This will create the file CORE_DIELECTRIC_IMAG.dat containing the sum of the imaginary part of the dielectric matrix.		This will create the file CORE_DIELECTRIC_IMAG.dat containing the sum of the imaginary part of the dielectric matrix.
	Note that the absolute values of the experimental peak positions is not captured due to fundamental limitations of local DFT to describe the core level energies. Usually, there is even a noticeable deviation between calculations using different codes. Therefore, it is accepted in literature to look at the relative peak positions in the spectra and their relative intensity.		Note that the absolute values of the experimental peak positions is not captured due to fundamental limitations of local DFT to describe the core level energies. Usually, there is even a noticeable deviation between calculations using different codes. Therefore, it is accepted in literature to look at the relative peak positions in the spectra and their relative intensity.

	We compare the results obtained with VASP to experimental<ref name="Ma.PRL"/> and theoretical<ref name="Tallefumier.PRB"/> XAS spectra from literature provided in the files ''C_XAS_aligned_to_VASP.dat'' and ''C_PARATEC_aligned_to_VASP.dat'', respectively. The theoretical reference calculation was obtained using the PARATEC code and relies on PAW/Pseudopotential similar to VASP. We provide a script with this tutorial to compare these literature results to the spectrum obtained with VASP		We compare the results obtained with VASP to experimental<ref name="Ma.PRL"/> and theoretical<ref name="Tallefumier.PRB"/> XAS spectra from literature provided in the files ''C_XAS_aligned_to_VASP.dat'' and ''C_PARATEC_aligned_to_VASP.dat'', respectively. The theoretical reference calculation was obtained using the PARATEC code and relies on PAW/Pseudopotential similar to VASP. We provide a script with this tutorial to compare these literature results to the spectrum obtained with VASP:
	gnuplot ~~gnuplot~~.script
			<div class="toccolours mw-customtoggle-script">'''Click to show/''gnuplot_XANES_C.script''</div>
			<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:gnuplot_XANES_C}}</div>

			To use that script type:
			gnuplot gnuplot_XANES_C.script
	The file ''plot.sh'' constitutes a convenient wrapper around these post processing steps. The resulting spectra should look like this:<br />		The file ''plot.sh'' constitutes a convenient wrapper around these post processing steps. The resulting spectra should look like this:<br />
	[[File:Fig XAS 4.png\|600px]]		[[File:Fig XAS 4.png\|600px]]

Karsai: /* Step 4 Extraction of XAS Spectrum */

2020-09-02T14:58:30Z

Step 4 Extraction of XAS Spectrum

← Older revision		Revision as of 14:58, 2 September 2020
Line 121:		Line 121:
	<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:plot_core_imdiel}}</div>		<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:plot_core_imdiel}}</div>

			To use it type:
			bash ./plot_core_imdiel.pl

	~~which~~ will create the file CORE_DIELECTRIC_IMAG.dat containing the sum of the imaginary part of the dielectric matrix.		This will create the file CORE_DIELECTRIC_IMAG.dat containing the sum of the imaginary part of the dielectric matrix.
	Note that the absolute values of the experimental peak positions is not captured due to fundamental limitations of local DFT to describe the core level energies. Usually, there is even a noticeable deviation between calculations using different codes. Therefore, it is accepted in literature to look at the relative peak positions in the spectra and their relative intensity.		Note that the absolute values of the experimental peak positions is not captured due to fundamental limitations of local DFT to describe the core level energies. Usually, there is even a noticeable deviation between calculations using different codes. Therefore, it is accepted in literature to look at the relative peak positions in the spectra and their relative intensity.

Karsai: /* Step 4 Extraction of XAS Spectrum */

2020-09-02T14:54:47Z

Step 4 Extraction of XAS Spectrum

← Older revision		Revision as of 14:54, 2 September 2020
Line 116:		Line 116:
	...		...

	Usually we are interested in the sum of all components of the dielectric matrix. You can obtain this by the script provided in this tutorial		Usually we are interested in the sum of all components of the dielectric matrix. You can obtain this by the script provided in this tutorial ''plot_core_imdiel.pl''
	~~perl .~~/plot_core_imdiel.pl
			<div class="toccolours mw-customtoggle-script">'''Click to show/''plot_core_imdiel.pl''</div>
			<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:plot_core_imdiel}}</div>


	which will create the file CORE_DIELECTRIC_IMAG.dat containing the sum of the imaginary part of the dielectric matrix.		which will create the file CORE_DIELECTRIC_IMAG.dat containing the sum of the imaginary part of the dielectric matrix.
	Note that the absolute values of the experimental peak positions is not captured due to fundamental limitations of local DFT to describe the core level energies. Usually, there is even a noticeable deviation between calculations using different codes. Therefore, it is accepted in literature to look at the relative peak positions in the spectra and their relative intensity.		Note that the absolute values of the experimental peak positions is not captured due to fundamental limitations of local DFT to describe the core level energies. Usually, there is even a noticeable deviation between calculations using different codes. Therefore, it is accepted in literature to look at the relative peak positions in the spectra and their relative intensity.

Karsai: /* References */

2019-11-14T14:21:52Z

References

← Older revision		Revision as of 14:21, 14 November 2019
Line 142:		Line 142:

	{{Template:XAS}}		{{Template:XAS}}

	~~Back to the [[The_VASP_Manual\|main page]].~~

	[[Category:Examples]]		[[Category:Examples]]

Karsai: /* Download */

2019-11-14T14:21:44Z

Download

← Older revision		Revision as of 14:21, 14 November 2019
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	== Download ==		== Download ==
	[~~http~~:~~//www.vasp.at/vasp-workshop/examples/~~XANES_Diamond.tgz XANES_Diamond.tgz]		[[Media:XANES_Diamond.tgz\| XANES_Diamond.tgz]]

	== References ==		== References ==

Karsai at 10:50, 4 October 2019

2019-10-04T10:50:39Z

← Older revision		Revision as of 10:50, 4 October 2019
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	~~(UNDER CONSTRUCTION)~~

	Important: This feature will be only available from VASP 6.0.		Important: This feature will be only available from VASP 6.0.