Modena 2025 : Yambopy part 1 - Revision history

FulvioPaleari at 19:46, 18 May 2025

2025-05-18T19:46:32Z

← Older revision		Revision as of 19:46, 18 May 2025
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	cd YAMBOPY_TUTORIALS		cd YAMBOPY_TUTORIALS
	rsync -avzP /leonardo_work/tra25_yambo/YAMBOPY_TUTORIALS/yambopy_tutorial_Modena_2025.tar.gz .		rsync -avzP /leonardo_work/tra25_yambo/YAMBOPY_TUTORIALS/yambopy_tutorial_Modena_2025.tar.gz .
	tar -xvzf yambopy_tutorial_Modena_2025.tar.gz		tar --strip-components=1 -xvzf yambopy_tutorial_Modena_2025.tar.gz

	= Plot band structures from Quantum ESPRESSO =		= Plot band structures from Quantum ESPRESSO =

FulvioPaleari at 17:32, 18 May 2025

2025-05-18T17:32:06Z

← Older revision		Revision as of 17:32, 18 May 2025
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	In order to run both parts 1 and 2, you need to copy and extract the tar file named '''yambopy_tutorial_Modena_2025.tar.gz''' that you find in the '''WORK''' directory:		In order to run both parts 1 and 2, you need to copy and extract the tar file named '''yambopy_tutorial_Modena_2025.tar.gz''' that you find in the '''WORK''' directory:
	cd $SCRATCH		cd $SCRATCH
	mkdir YAMBOPY_TUTORIALS		mkdir -p YAMBOPY_TUTORIALS
	cd YAMBOPY_TUTORIALS		cd YAMBOPY_TUTORIALS
	rsync -avzP /leonardo_work/tra25_yambo/YAMBOPY_TUTORIALS/yambopy_tutorial_Modena_2025.tar.gz .		rsync -avzP /leonardo_work/tra25_yambo/YAMBOPY_TUTORIALS/yambopy_tutorial_Modena_2025.tar.gz .

FulvioPaleari: /* Tutorial 3: generating the Yambo SAVE via command line */

2025-05-18T17:27:01Z

Tutorial 3: generating the Yambo SAVE via command line

← Older revision		Revision as of 17:27, 18 May 2025
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	Remember to load the yambo module, so that yambopy has access to the '''p2y''' and '''yambo''' executables.		Remember to load the yambo module, so that yambopy has access to the '''p2y''' and '''yambo''' executables.
			module use /leonardo/pub/userexternal/nspallan/spack-0.22.2-06/modules
			module load yambo/5.3.0--intel-oneapi-mpi--2021.12.1--oneapi--2024.1.0

	The quantum espresso save for hBN is provided in the directory <code>BSE_saves/QE_saves/hBN.save</code> (you can check the contents of the various folders).		The quantum espresso save for hBN is provided in the directory <code>BSE_saves/QE_saves/hBN.save</code> (you can check the contents of the various folders).
	Then, following the instructions printed on screen, we can generate a yambo SAVE from the hBN.save by typing		Then, following the instructions printed on screen, we can generate a yambo SAVE from the hBN.save by typing

FulvioPaleari at 17:25, 18 May 2025

2025-05-18T17:25:32Z

← Older revision		Revision as of 17:25, 18 May 2025
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	As you can see, at small momenta the inverse dielectric function sharply rises to 1 in a 2D system. This is why a very dense reciprocal-space sampling (or advanced techniques such as the RIM-W) is required to converge it.		As you can see, at small momenta the inverse dielectric function sharply rises to 1 in a 2D system. This is why a very dense reciprocal-space sampling (or advanced techniques such as the RIM-W) is required to converge it.

	==Links==		=Links=
	* Proceed to [[Modena 2025 : Yambopy part 2]]		* Proceed to [[Modena 2025 : Yambopy part 2]]
	* Back to [[Modena 2025]]		* Back to [[Modena 2025]]

FulvioPaleari at 17:07, 18 May 2025

2025-05-18T17:07:15Z

← Older revision		Revision as of 17:07, 18 May 2025
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	==Links==		==Links==
			* Proceed to [[Modena 2025 : Yambopy part 2]]
	* Back to [[Modena 2025]]		* Back to [[Modena 2025]]

FulvioPaleari at 17:05, 18 May 2025

2025-05-18T17:05:21Z

← Older revision		Revision as of 17:05, 18 May 2025
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	yem1s.plot_epsm1(ax1,ng1=0,ng2=0,ls='-',marker='o')		yem1s.plot_epsm1(ax1,ng1=0,ng2=0,ls='-',marker='o')

	[[File:BN RPA em1s.png~~\|thumb~~\|Yambo inverse dielectric function plot\|500px]]		[[File:BN RPA em1s.png\|Yambo inverse dielectric function plot\|500px]]

	As you can see, at small momenta the inverse dielectric function sharply rises to 1 in a 2D system. This is why a very dense reciprocal-space sampling (or advanced techniques such as the RIM-W) is required to converge it.		As you can see, at small momenta the inverse dielectric function sharply rises to 1 in a 2D system. This is why a very dense reciprocal-space sampling (or advanced techniques such as the RIM-W) is required to converge it.

FulvioPaleari: /* Tutorial 6: Dielectric function */

2025-05-18T17:04:51Z

Tutorial 6: Dielectric function

← Older revision		Revision as of 17:04, 18 May 2025
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	yem1s.plot_epsm1(ax1,ng1=0,ng2=0,ls='-',marker='o')		yem1s.plot_epsm1(ax1,ng1=0,ng2=0,ls='-',marker='o')

	[[File:~~Em1s hbn~~.png\|~~Inverse~~ dielectric function plot ~~from yambopy tutorial~~\|500px]]		[[File:BN RPA em1s.png\|thumb\|Yambo inverse dielectric function plot\|500px]]

	As you can see, at small momenta the inverse dielectric function sharply rises to 1 in a 2D system. This is why a very dense reciprocal-space sampling (or advanced techniques such as the RIM-W) is required to converge it.		As you can see, at small momenta the inverse dielectric function sharply rises to 1 in a 2D system. This is why a very dense reciprocal-space sampling (or advanced techniques such as the RIM-W) is required to converge it.


	==Links==		==Links==
	* Back to [[Modena 2025]]		* Back to [[Modena 2025]]

FulvioPaleari at 17:01, 18 May 2025

2025-05-18T17:01:10Z

← Older revision		Revision as of 17:01, 18 May 2025
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	=== Tutorial 5: Dipoles intro (plots of dipoles on BZ, plot of IP absorption) ===		== Tutorial 5: Dipoles intro (plots of dipoles on BZ, plot of IP absorption) ==
	In this section we will use the script <code>dipoles_plot.py</code> and read the dipole databases generated in an optical absorption calculation by yambo. Keep in mind that from now on we will use the "BSE" yambo SAVE generated in the [[#Command line: generating the Yambo SAVE\|first section]].		In this section we will use the script <code>dipoles_plot.py</code> and read the dipole databases generated in an optical absorption calculation by yambo. Keep in mind that from now on we will use the "BSE" yambo SAVE generated in the [[#Command line: generating the Yambo SAVE\|first section]].

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	[[File:Dipoles hbn2.png\|YamboDipolesDB plot from yambopy tutorial\|500px]]		[[File:Dipoles hbn2.png\|YamboDipolesDB plot from yambopy tutorial\|500px]]

	=== Tutorial 6: Dielectric function ===		== Tutorial 6: Dielectric function ==
	The dielectric function in the RPA approximation is a crucial quantity that yambo needs to compute both for GW calculations (including its frequency dependence via plasmon-pole approximation or more advanced methods) and BSE spectra (here only the static part is needed).		The dielectric function in the RPA approximation is a crucial quantity that yambo needs to compute both for GW calculations (including its frequency dependence via plasmon-pole approximation or more advanced methods) and BSE spectra (here only the static part is needed).

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	We can read these databases with the class <code>YamboStaticScreeningDB</code> as it is done in the script '''em1s.py'''. The docstring of the script provides useful information into the form in which the dielectric function is actually stored and how to convert into either the inverse microscopic dielectric function (a tensor in G-space) or the macroscopic dielectric function itself.		We can read these databases with the class <code>YamboStaticScreeningDB</code> as it is done in the script '''em1s.py'''. The docstring of the script provides useful information into the form in which the dielectric function is actually stored and how to convert into either the inverse microscopic dielectric function (a tensor in G-space) or the macroscopic dielectric function itself.

	You can then produce a plot of these quantities for 2D hBN (below the inverse dielectric function).		yem1s = YamboStaticScreeningDB(save=save_path+'/SAVE',em1s=bse_path)

			Printing information on this object returns the main information needed to understand the origin of the database: number of bands included, number of reciprocal lattice vectors, type of 2D cutoff used (if any), etc.

			print(yem1s)

			You can then produce a plot of these quantities for 2D hBN (below the head of the inverse dielectric function):

			yem1s.plot_epsm1(ax1,ng1=0,ng2=0,ls='-',marker='o')

	[[File:Em1s hbn.png\|Inverse dielectric function plot from yambopy tutorial\|500px]]		[[File:Em1s hbn.png\|Inverse dielectric function plot from yambopy tutorial\|500px]]

FulvioPaleari at 16:57, 18 May 2025

2025-05-18T16:57:37Z

@@ Line 263: / Line 263: @@
 [[File:Dipoles hbn2.png|YamboDipolesDB plot from yambopy tutorial|500px]]
 ==Links==
 * Back to [[Modena 2025]]

FulvioPaleari: /* Tutorial 4: Lattice intro (plot k-point coordinates in IBZ/BZ) */

2025-05-18T16:48:40Z

Tutorial 4: Lattice intro (plot k-point coordinates in IBZ/BZ)

← Older revision		Revision as of 16:48, 18 May 2025
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	* Scatterplot of the k-points in crystal coordinates [<code>Crystal_Plot=True</code>].		* Scatterplot of the k-points in crystal coordinates [<code>Crystal_Plot=True</code>].
	* Manual transformation of a chosen k-point from irreducible to full Brillouin zone (you can change the index <code>i_k</code> in the script to check different cases) [<code>Symmetry_Plot=True</code>].		* Manual transformation of a chosen k-point from irreducible to full Brillouin zone (you can change the index <code>i_k</code> in the script to check different cases) [<code>Symmetry_Plot=True</code>].

			Have a look at the script to understand which methods and attributed of the class '''YamboLatticeDB''' are used.

	[[File:Car kpoints hbn.jpg\|YamboLatticeDB plot from yambopy tutorial\| 500px]]		[[File:Car kpoints hbn.jpg\|YamboLatticeDB plot from yambopy tutorial\| 500px]]


	=== Dipoles intro: plots of dipoles on BZ, plot of IP absorption ===		=== Tutorial 5: Dipoles intro (plots of dipoles on BZ, plot of IP absorption) ===
	In this section we will use the script <code>dipoles_plot.py</code> and read the dipole databases generated in an optical absorption calculation by yambo. Keep in mind that from now on we will use the "BSE" yambo SAVE generated in the [[#Command line: generating the Yambo SAVE\|first section]].		In this section we will use the script <code>dipoles_plot.py</code> and read the dipole databases generated in an optical absorption calculation by yambo. Keep in mind that from now on we will use the "BSE" yambo SAVE generated in the [[#Command line: generating the Yambo SAVE\|first section]].

	The databases written after a calculation of optical properties with yambo (dipoles, ~~static screening~~, excitons) are in the directory <code>BSE_saves/BSE_databases</code>. Here we will also find <code>ndb.dipoles</code> which is needed now, since it contains the matrix elements d_{vck}(\alpha) where vk and ck are the valence and electron states involved in the transition and \alpha the polarisation direction of the external electric field.		The databases written after a calculation of optical properties with yambo (dipoles, RPA dielectric function, excitons) are in the directory <code>BSE_saves/BSE_databases</code>. Here we will also find <code>ndb.dipoles</code> which is needed now, since it contains the matrix elements d_{vck}(\alpha) where vk and ck are the valence and electron states involved in the transition and \alpha the polarisation direction of the external electric field.

	In order to read it in python we use the Yambopy class <code>YamboDipolesDB</code>, which can be instanced like this:		In order to read it in python we use the Yambopy class <code>YamboDipolesDB</code>, which can be instanced like this:
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	[[File:Dipoles hbn2.png\|YamboDipolesDB plot from yambopy tutorial\|500px]]		[[File:Dipoles hbn2.png\|YamboDipolesDB plot from yambopy tutorial\|500px]]



	==Links==		==Links==
	* Back to [[Modena 2025]]		* Back to [[Modena 2025]]