Dichroism in molecules - Revision history

Davide: /* Few equations */

2024-06-21T13:46:56Z

Few equations

← Older revision		Revision as of 13:46, 21 June 2024
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	== Few equations ==		== Few equations ==

	NCD is described by the trace of the so called beta tensor ~~<br>~~		NCD is described by the trace of the so called beta tensor
	[[File:Deltan Beta relation.png\|x60px\|frameless\|Yambo tutorial image]] ~~<br>~~
			[[File:Deltan Beta relation.png\|x60px\|frameless\|Yambo tutorial image]]

	which related the electronic dipole to the time derivative of the applied magnetic field, and the magnetic dipole to the time derivative of the applied electric field		which related the electronic dipole to the time derivative of the applied magnetic field, and the magnetic dipole to the time derivative of the applied electric field
	[[File:Dipoles fields relations.png\|x120px\|frameless\|Yambo tutorial image]] ~~<br>~~
			[[File:Dipoles fields relations.png\|x120px\|frameless\|Yambo tutorial image]]

	The latter can be obtained via the so called G tensor, which is similar to the dipole-dipole response function, but with electric and magnetic dipoles		The latter can be obtained via the so called G tensor, which is similar to the dipole-dipole response function, but with electric and magnetic dipoles

Davide: /* Few equations */

2024-06-21T09:10:12Z

Few equations

← Older revision		Revision as of 09:10, 21 June 2024
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	NCD is described by the trace of the so called beta tensor <br>		NCD is described by the trace of the so called beta tensor <br>
	[[File:Deltan Beta relation.png\|x60px\|frameless\|Yambo tutorial image]] <br>		[[File:Deltan Beta relation.png\|x60px\|frameless\|Yambo tutorial image]] <br>
	which related ~~the change in~~ the electronic dipole to the time derivative of the applied magnetic field, and the magnetic dipole to the time derivative of the applied electric field		which related the electronic dipole to the time derivative of the applied magnetic field, and the magnetic dipole to the time derivative of the applied electric field
	[[File:Dipoles fields relations.png\|x120px\|frameless\|Yambo tutorial image]] <br>		[[File:Dipoles fields relations.png\|x120px\|frameless\|Yambo tutorial image]] <br>

Davide: Added initial equation

2024-06-21T09:07:55Z

Added initial equation

← Older revision		Revision as of 09:07, 21 June 2024
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	~~'''WARNING~~: ~~under construction'''~~		[[File:Chirality with hands.svg\|x300px\|frameless\|right\|Chirality representation with hands, from wikipedia]]

	[[File:~~Chirality with hands~~.~~svg~~\|~~x300px~~\|frameless\|~~right\|Chirality representation with hands, from wikipedia~~]]		Circular dichroism (CD) is dichroism involving circularly polarized light, i.e., the differential absorption of left- and right-handed light<ref name="wiki_CD"/>.

			[[File:Deltan equation.png\|x30px\|frameless\|Yambo tutorial image]]

	~~Circular dichroism (CD) is dichroism involving circularly polarized light, i.e., the differential absorption of left- and right-handed light<ref name="wiki_CD"/>.~~ Dichroism in absorption can originate from an asymmetry in the dielectric tensor, which can be induced by the presence of either an external magnetic field or a spontaneous magnetization (MCD). This can be computed from the off-diagonal elements of the dielectric tensor. See the tutorial on [[The magneto-optical Kerr effect]] (MOKE). Another form of dichroism can be due to the chiral nature of molecules or materials<ref name="wiki_chiral"/> and goes under the name of natural circular dichroism (NCD). This latter can be related to the beta tensor and will be discussed in the present tutorial.		Dichroism in absorption can originate from an asymmetry in the dielectric tensor, which can be induced by the presence of either an external magnetic field or a spontaneous magnetization (MCD). This can be computed from the off-diagonal elements of the dielectric tensor. See the tutorial on [[The magneto-optical Kerr effect]] (MOKE). Another form of dichroism can be due to the chiral nature of molecules or materials<ref name="wiki_chiral"/> and goes under the name of natural circular dichroism (NCD). This latter can be related to the beta tensor and will be discussed in the present tutorial.

	== Few equations ==		== Few equations ==
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	NCD is described by the trace of the so called beta tensor <br>		NCD is described by the trace of the so called beta tensor <br>
	[[File:Deltan Beta relation.png\|x60px\|frameless\|Yambo tutorial image]] <br>		[[File:Deltan Beta relation.png\|x60px\|frameless\|Yambo tutorial image]] <br>
	which related the change in the electronic dipole to the time derivative of the applied magnetic field, and the magnetic dipole to the time derivative of the applied electric field ~~<br>~~		which related the change in the electronic dipole to the time derivative of the applied magnetic field, and the magnetic dipole to the time derivative of the applied electric field
	[[File:Dipoles fields relations.png\|x120px\|frameless\|Yambo tutorial image]] <br>		[[File:Dipoles fields relations.png\|x120px\|frameless\|Yambo tutorial image]] <br>

	The latter can be obtained via the so called G tensor, which is similar to the dipole-dipole response function, but with electric and magnetic dipoles ~~<br>~~		The latter can be obtained via the so called G tensor, which is similar to the dipole-dipole response function, but with electric and magnetic dipoles

	[[File:Beta G tensor relation.png\|x60px\|frameless\|Beta G tensor relation]] <br>		[[File:Beta G tensor relation.png\|x60px\|frameless\|Beta G tensor relation]] <br>
	[[File:Gtensor.png\|x120px\|frameless\|Yambo tutorial image]] <br>		[[File:Gtensor.png\|x120px\|frameless\|Yambo tutorial image]] <br>

	The calculation of the magnetic dipoles is what makes NCD difficult to be computed in PBC, since these are not easily defined (solutions have been recently proposed in the literature). For isolated systems instead a simple sum over states can be employed (this is not possible in PBC because it involves diagonal intra-band dipoles): <br>		The calculation of the magnetic dipoles is what makes NCD difficult to be computed in PBC, since these are not easily defined (solutions have been recently proposed in the literature). For isolated systems instead a simple sum over states can be employed (this is not possible in PBC because it involves diagonal intra-band dipoles): <br>
	[[File:Mdipoles sum over states.png\|x70px\|frameless\|Yambo tutorial image]]		[[File:Mdipoles sum over states.png\|x70px\|frameless\|Yambo tutorial image]]

			A detailed study of the convergence of the sum over states can be found in Ref.<ref name="Molteni2022"/>. The same approach is also used in the Siesta code.

	== Prerequisites ==		== Prerequisites ==
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	* Yambo core databases (9 Mb): [https://media.yambo-code.eu/educational/tutorials/files/R_methyloxirane_DBs.tar.gz R_methyloxirane_DBs.tar.gz]		* Yambo core databases (9 Mb): [https://media.yambo-code.eu/educational/tutorials/files/R_methyloxirane_DBs.tar.gz R_methyloxirane_DBs.tar.gz]

			<!--
	Alternatively you can re-generate the DB by your-self (also because the DB provided have been generated with small convergence parameters). To this end you just need to download and compile quantum espresso, and generate the DB using the input files and the pseudo-potentials provided. '''(TODO: input files still missing)'''		Alternatively you can re-generate the DB by your-self (also because the DB provided have been generated with small convergence parameters). To this end you just need to download and compile quantum espresso, and generate the DB using the input files and the pseudo-potentials provided. '''(TODO: input files still missing)'''
			-->

	=== Input files ===		=== Input files ===
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	BSEprop= "abs <span style="color:red">dich trace</span>" # [BSS] abs/kerr/magn/dichr trace		BSEprop= "abs <span style="color:red">dich trace</span>" # [BSS] abs/kerr/magn/dichr trace

	Since the dipoles are obtained from a sum over states it is important to converge the number of states used in the equation, this can be controlled via the input ~~variable~~		Since the dipoles are obtained from a sum over states it is important to converge the number of states used in the equation, this can be controlled via the input variables
	<span style="color:red">DipBandsALL</span> # [DIP] Compute all bands range, not only valence and conduction		<span style="color:red">DipBandsALL</span> # [DIP] Compute all bands range, not only valence and conduction
	DipApproach= "G-space v" # [DIP] [G-space v/R-space x/Covariant/Shifted grids]		DipApproach= "G-space v" # [DIP] [G-space v/R-space x/Covariant/Shifted grids]
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	%		%

	A standard input file for response function in transition space is (IP approximation		A standard input file for response function in transition space is (IP approximation)
	optics # [R] Linear Response optical properties		optics # [R] Linear Response optical properties
	bse # [R][BSE] Bethe Salpeter Equation.		bse # [R][BSE] Bethe Salpeter Equation.
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	Using the input file provided above you will obtain the following plots for absorption (alpha file, on the left) and NCD (CD file, on the right):		Using the input file provided above you will obtain the following plots for absorption (alpha file, on the left) and NCD (CD file, on the right):
	{\|style="margin: 10px auto;"		{\|style="margin: 10px auto;"
	\| [[File:Methylox abs tuto.png\|~~400px~~\|frameless\|center\|Yambo tutorial, absorption in methyloxirane]]		\| [[File:Methylox abs tuto.png\|450px\|frameless\|center\|Yambo tutorial, absorption in methyloxirane]]
	\| [[File:Methylox cd tuto.png\|~~400px~~\|frameless\|center\|Yambo tutorial, circular dichroism in methyloxirane]]		\| [[File:Methylox cd tuto.png\|450px\|frameless\|center\|Yambo tutorial, circular dichroism in methyloxirane]]
	\|}		\|}

Davide: /* Few equations */ Equations section created

2024-06-21T09:02:02Z

Few equations: Equations section created

← Older revision		Revision as of 09:02, 21 June 2024
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	== Few equations ==		== Few equations ==

			NCD is described by the trace of the so called beta tensor <br>
			[[File:Deltan Beta relation.png\|x60px\|frameless\|Yambo tutorial image]] <br>
			which related the change in the electronic dipole to the time derivative of the applied magnetic field, and the magnetic dipole to the time derivative of the applied electric field <br>
			[[File:Dipoles fields relations.png\|x120px\|frameless\|Yambo tutorial image]] <br>

			The latter can be obtained via the so called G tensor, which is similar to the dipole-dipole response function, but with electric and magnetic dipoles <br>
			[[File:Beta G tensor relation.png\|x60px\|frameless\|Beta G tensor relation]] <br>
			[[File:Gtensor.png\|x120px\|frameless\|Yambo tutorial image]] <br>

			The calculation of the magnetic dipoles is what makes NCD difficult to be computed in PBC, since these are not easily defined (solutions have been recently proposed in the literature). For isolated systems instead a simple sum over states can be employed (this is not possible in PBC because it involves diagonal intra-band dipoles): <br>
			[[File:Mdipoles sum over states.png\|x70px\|frameless\|Yambo tutorial image]]

	== Prerequisites ==		== Prerequisites ==

Davide: /* Input files */

2024-06-18T16:31:10Z

Input files

← Older revision		Revision as of 16:31, 18 June 2024
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	=== Input files ===		=== Input files ===
	To compute NCD a standard calculation of response function in transition space needs to be ~~performend~~, ~~with~~ the ~~sole extra~~ variable		To compute NCD a standard calculation of response function in transition space needs to be performed, also setting "dich" (short for dichroism) and eventually "trace" in the "BSE_prop" variable as below
	BSEprop= "abs <span style="color:red">dich trace</span>" # [BSS] abs/kerr/magn/dichr trace		BSEprop= "abs <span style="color:red">dich trace</span>" # [BSS] abs/kerr/magn/dichr trace

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	CUTCylLen= 0.000000 # [CUT] [au] Cylinder length		CUTCylLen= 0.000000 # [CUT] [au] Cylinder length
	CUTwsGvec= 0.700000 # [CUT] WS cutoff: number of G to be modified		CUTwsGvec= 0.700000 # [CUT] WS cutoff: number of G to be modified


	== Methyloxirane ==		== Methyloxirane ==

Davide: Fixing wikipedia references

2024-06-18T16:29:21Z

Fixing wikipedia references

← Older revision		Revision as of 16:29, 18 June 2024
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	[[File:Chirality with hands.svg\|x300px\|frameless\|right\|Chirality representation with hands, from wikipedia]]		[[File:Chirality with hands.svg\|x300px\|frameless\|right\|Chirality representation with hands, from wikipedia]]

	Circular dichroism (CD) is dichroism involving circularly polarized light, i.e., the differential absorption of left- and right-handed light<ref name="~~wikipedia1~~"/>. Dichroism in absorption can originate from an asymmetry in the dielectric tensor, which can be induced by the presence of either an external magnetic field or a spontaneous magnetization (MCD). This can be computed from the off-diagonal elements of the dielectric tensor. See the tutorial on [[The magneto-optical Kerr effect]] (MOKE). Another form of dichroism can be due to the chiral nature of molecules or materials<ref name="~~wikipedia2~~"/> and goes under the name of natural circular dichroism (NCD). This latter can be related to the beta tensor and will be discussed in the present tutorial.		Circular dichroism (CD) is dichroism involving circularly polarized light, i.e., the differential absorption of left- and right-handed light<ref name="wiki_CD"/>. Dichroism in absorption can originate from an asymmetry in the dielectric tensor, which can be induced by the presence of either an external magnetic field or a spontaneous magnetization (MCD). This can be computed from the off-diagonal elements of the dielectric tensor. See the tutorial on [[The magneto-optical Kerr effect]] (MOKE). Another form of dichroism can be due to the chiral nature of molecules or materials<ref name="wiki_chiral"/> and goes under the name of natural circular dichroism (NCD). This latter can be related to the beta tensor and will be discussed in the present tutorial.

	== Few equations ==		== Few equations ==
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	=== Databases ===		=== Databases ===
	[[File:R methyloxirane structure.png\|x150px\|frameless\|right\|R methyloxirane structure]]		[[File:R methyloxirane structure.png\|x150px\|frameless\|right\|R methyloxirane structure]]
	In this tutorial we will compute NCD on Propylene oxide, also known as R-Methyloxirane. R-Methyloxirane has often been used in the literature as a benchmark molecule for NCD calculations against experimental data, due to its rigidity. To this end we provide a <code>yambo</code> database (DB) for R_methyloxirane.		In this tutorial we will compute NCD on Propylene oxide, also known as R-Methyloxirane<ref name="wiki_PropOxide"/>. R-Methyloxirane has often been used in the literature as a benchmark molecule for NCD calculations against experimental data, due to its rigidity. To this end we provide a <code>yambo</code> database (DB) for R_methyloxirane.

	* Yambo core databases (9 Mb): [https://media.yambo-code.eu/educational/tutorials/files/R_methyloxirane_DBs.tar.gz R_methyloxirane_DBs.tar.gz]		* Yambo core databases (9 Mb): [https://media.yambo-code.eu/educational/tutorials/files/R_methyloxirane_DBs.tar.gz R_methyloxirane_DBs.tar.gz]
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	<references>		<references>
	<ref name="~~wikipedia1~~">[https://en.wikipedia.org/wiki/Circular_dichroism Circular Dichroism] on wikipedia</ref>		<ref name="wiki_CD">[https://en.wikipedia.org/wiki/Circular_dichroism Circular Dichroism] on wikipedia</ref>
	<ref name="~~wikipedia2~~">[https://en.wikipedia.org/wiki/Chiral_media Chiral Media] on wikipedia</ref>		<ref name="wiki_chiral">[https://en.wikipedia.org/wiki/Chiral_media Chiral Media] on wikipedia</ref>
			<ref name="wiki_PropOxide">[https://en.wikipedia.org/wiki/Propylene_oxide Propylene oxide] on wikipedia</ref>
	<ref name="Molteni2022">E. Molteni, G. Cappellini, and D. Sangalli, ''Ab initio circular dichroism with the Yambo code: applications to dipeptides'', [https://www.doi.org/10.1088/1757-899X/1265/1/012005 IOP Conf. Series: Materials Science and Engineering 1265, 012005 (2022)]</ref>		<ref name="Molteni2022">E. Molteni, G. Cappellini, and D. Sangalli, ''Ab initio circular dichroism with the Yambo code: applications to dipeptides'', [https://www.doi.org/10.1088/1757-899X/1265/1/012005 IOP Conf. Series: Materials Science and Engineering 1265, 012005 (2022)]</ref>
	</references>		</references>

Davide: /* Databases */

2024-06-18T16:27:07Z

Databases

← Older revision		Revision as of 16:27, 18 June 2024
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	=== Databases ===		=== Databases ===
	[[File:R methyloxirane structure.png\|x150px\|frameless\|right\|R methyloxirane structure]]		[[File:R methyloxirane structure.png\|x150px\|frameless\|right\|R methyloxirane structure]]
	~~For~~ this ~~tutorials~~ we provide a <code>yambo</code> database (DB) for R_methyloxirane.		In this tutorial we will compute NCD on Propylene oxide, also known as R-Methyloxirane. R-Methyloxirane has often been used in the literature as a benchmark molecule for NCD calculations against experimental data, due to its rigidity. To this end we provide a <code>yambo</code> database (DB) for R_methyloxirane.

	* Yambo core databases (9 Mb): [https://media.yambo-code.eu/educational/tutorials/files/R_methyloxirane_DBs.tar.gz R_methyloxirane_DBs.tar.gz]		* Yambo core databases (9 Mb): [https://media.yambo-code.eu/educational/tutorials/files/R_methyloxirane_DBs.tar.gz R_methyloxirane_DBs.tar.gz]

Davide: /* CD at the Independent Particles approximation */

2024-06-18T16:25:53Z

CD at the Independent Particles approximation

← Older revision		Revision as of 16:25, 18 June 2024
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	=== CD at the Independent Particles approximation ===		=== CD at the Independent Particles approximation ===
	~~Methyloxirane has often been used in the literature as a benchmark molecule for NCD calculations against experimental data, due to its rigidity.~~ Here we use it to show how to compute NCD using the yambo code.		Here we use it to show how to compute NCD using the yambo code.
	Here we provide a poorly converged database, just to show how a calculation of NCD works with the yambo code.		Here we provide a poorly converged database, just to show how a calculation of NCD works with the yambo code.
	Using the input file provided above you will obtain the following plots for absorption (alpha file, on the left) and NCD (CD file, on the right):		Using the input file provided above you will obtain the following plots for absorption (alpha file, on the left) and NCD (CD file, on the right):

Davide: Equations section moved above

2024-06-18T16:22:52Z

Equations section moved above

← Older revision		Revision as of 16:22, 18 June 2024
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	Circular dichroism (CD) is dichroism involving circularly polarized light, i.e., the differential absorption of left- and right-handed light<ref name="wikipedia1"/>. Dichroism in absorption can originate from an asymmetry in the dielectric tensor, which can be induced by the presence of either an external magnetic field or a spontaneous magnetization (MCD). This can be computed from the off-diagonal elements of the dielectric tensor. See the tutorial on [[The magneto-optical Kerr effect]] (MOKE). Another form of dichroism can be due to the chiral nature of molecules or materials<ref name="wikipedia2"/> and goes under the name of natural circular dichroism (NCD). This latter can be related to the beta tensor and will be discussed in the present tutorial.		Circular dichroism (CD) is dichroism involving circularly polarized light, i.e., the differential absorption of left- and right-handed light<ref name="wikipedia1"/>. Dichroism in absorption can originate from an asymmetry in the dielectric tensor, which can be induced by the presence of either an external magnetic field or a spontaneous magnetization (MCD). This can be computed from the off-diagonal elements of the dielectric tensor. See the tutorial on [[The magneto-optical Kerr effect]] (MOKE). Another form of dichroism can be due to the chiral nature of molecules or materials<ref name="wikipedia2"/> and goes under the name of natural circular dichroism (NCD). This latter can be related to the beta tensor and will be discussed in the present tutorial.

			== Few equations ==


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	CUTwsGvec= 0.700000 # [CUT] WS cutoff: number of G to be modified		CUTwsGvec= 0.700000 # [CUT] WS cutoff: number of G to be modified

	~~== Few equations ==~~

	== Methyloxirane ==		== Methyloxirane ==

Davide: Added image of methyloxirane

2024-06-18T16:21:44Z

Added image of methyloxirane

← Older revision		Revision as of 16:21, 18 June 2024
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	== Prerequisites ==		== Prerequisites ==
	=== Databases ===		=== Databases ===
			[[File:R methyloxirane structure.png\|x150px\|frameless\|right\|R methyloxirane structure]]
	For this tutorials we provide a <code>yambo</code> database (DB) for R_methyloxirane.		For this tutorials we provide a <code>yambo</code> database (DB) for R_methyloxirane.