Hydrogen chain - Revision history

Davide: /* Prerequisites */ Link fixed

2023-11-17T09:16:02Z

Prerequisites: Link fixed

← Older revision		Revision as of 09:16, 17 November 2023
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	== Prerequisites ==		== Prerequisites ==
	* The <code>SAVE</code> databases for the hydrogen chain: [http://~~www~~.yambo-code.~~org~~/educational/tutorials/files/Hydrogen_Chain.tar.gz Hydrogen_Chain.tar.gz]		* The <code>SAVE</code> databases for the hydrogen chain: [http://media.yambo-code.eu/educational/tutorials/files/Hydrogen_Chain.tar.gz Hydrogen_Chain.tar.gz]
	* The <code>yambo</code> and <code>ypp</code> executables		* The <code>yambo</code> and <code>ypp</code> executables
	* <code>gnuplot</code> and [http://www.xcrysden.org <code>xcrysden</code>], for plotting spectra and electron densities		* <code>gnuplot</code> and [http://www.xcrysden.org <code>xcrysden</code>], for plotting spectra and electron densities

Conor at 16:44, 6 November 2019

2019-11-06T16:44:36Z

Show changes

Marini at 11:53, 6 November 2019

2019-11-06T11:53:03Z

← Older revision		Revision as of 11:53, 6 November 2019
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	In this tutorial you will learn why ALDA fails in extended systems as well as general strategies for treating 1D systems.		In this tutorial you will learn why ALDA fails in extended systems as well as general strategies for treating 1D systems.

	~~<!-- [Tutorial [[../files/hydrogen_chain.pdf\|pdf]] document] -->~~

	~~<!-- In the first TDDFT [[../tddft/index.php\|tutorial]] we learned how to calculate the response function in the TDDFT scheme.~~
	You should have noticed that the performance of the ALDA gradually worsens moving from 0 to 3 dimensions. This means that the drawbacks of the approximation are somehow due to possibility that the electrons move in "wider" regions of space.<br /> -->

	== Background ==		== Background ==
Line 30:		Line 25:

	Enter the 2.05 directory and run the initialization step		Enter the 2.05 directory and run the initialization step
	$ cd YAMBO/2.05		> cd YAMBO/2.05
	$ ls		> ls
	BSE/ SAVE/		BSE/ SAVE/
	$ yambo ''(initialization)''		> yambo ''(initialization)''

	From reading the r_setup file we notice that the system has a small (0.27 eV) gap. Now generate the input file for the TDLDA calculation by typing		From reading the r_setup file we notice that the system has a small (0.27 eV) gap. Now generate the input file for the TDLDA calculation by typing
	$ yambo -o b -k alda -y d -V qp -F in_alda
			> yambo -o b -k alda -y d -V qp -F in_alda

	and change the highlighted lines in the input file:		and change the highlighted lines in the input file:

	optics # [R OPT] Optics		optics # [R OPT] Optics
	bse # [R BSK] Bethe Salpeter Equation.		bse # [R BSK] Bethe Salpeter Equation.
Line 50:		Line 49:
	BEnSteps= '''1000''' # [BSS] Energy steps		BEnSteps= '''1000''' # [BSS] Energy steps
	Now use the ''resp'' verbosity to activate the flag needed to dump to file the eigenvectors of the BS Hamiltonian		Now use the ''resp'' verbosity to activate the flag needed to dump to file the eigenvectors of the BS Hamiltonian
	$ yambo -o b -t a -y d -V resp -F in_alda
			> yambo -o b -t a -y d -V resp -F in_alda

	and remove the ''#'' from the appropriate flag to activate the option:		and remove the ''#'' from the appropriate flag to activate the option:

	#WRbsWF # [BSS] Write to disk excitonic the FWs		#WRbsWF # [BSS] Write to disk excitonic the FWs

Line 66:		Line 68:
	Now, please, repeat the same procedure in the 2.5 folder		Now, please, repeat the same procedure in the 2.5 folder

	$ cd ../2.5		> cd ../2.5
	$ yambo		> yambo
	$ yambo -o b -t a -y d -V resp -F in_alda		> yambo -o b -t a -y d -V resp -F in_alda

	modify the input file and run again <code>yambo</code>.		modify the input file and run again <code>yambo</code>.
Line 87:		Line 89:
	To this end we can use the yambo post/pre processor (YPP). <code>ypp</code> is capable of performing some basic analyses using the pre-calculated informations stored in the yambo databases.<br />		To this end we can use the yambo post/pre processor (YPP). <code>ypp</code> is capable of performing some basic analyses using the pre-calculated informations stored in the yambo databases.<br />
	YPP works like yambo. It uses a series of options to create an input file containing only the variables that are relevant to that type of calculation. Launch it with the help (-H) flag to see a full list of options.		YPP works like yambo. It uses a series of options to create an input file containing only the variables that are relevant to that type of calculation. Launch it with the help (-H) flag to see a full list of options.

	> cd 2.05/		> cd 2.05/
	> ypp -H		> ypp -H

	To plot the density we need to type		To plot the density we need to type
	> ypp -s d
	The input file ''~~ypp.in~~'' will be		> ypp -s d -F in_density

			The input file ''in_density'' will be

	electrons # [R] Electrons (and holes)		electrons # [R] Electrons (and holes)
Line 104:		Line 109:
	To use XCrysden switch to "x" the value of the ''Format'' variable.<br />		To use XCrysden switch to "x" the value of the ''Format'' variable.<br />
	Now you can launch ypp.		Now you can launch ypp.

	> ypp		> ypp -F in_density

	At the end of the quick calculation you will find in your directory the file ''o.density_2d.xsf'' that you can plot using Xcrysden.		At the end of the quick calculation you will find in your directory the file ''o.density_2d.xsf'' that you can plot using Xcrysden.
Line 171:		Line 176:
	> ypp -F in_tdlda_density -J ALDA		> ypp -F in_tdlda_density -J ALDA

	it will create the file ''o-ALDA.exc_3d_1.xsf'' that you can plot by using		'''remembering to put the ALDA jobstring to allow Yambo to find the ALDA databases'''. This will create the file ''o-ALDA.exc_3d_1.xsf'' that you can plot by using

	> launch_xcrysden.sh o-ALDA.exc_3d_1.xsf		> launch_xcrysden.sh o-ALDA.exc_3d_1.xsf
Line 215:		Line 220:

	> cd 2.5		> cd 2.5
	> yambo -o c -k lrc		> yambo -o c -k lrc -F in_LRC

	Change the highlighted variables in the input file:		Change the highlighted variables in the input file:
Line 257:		Line 262:
	We start by generating the input file. At the command line we have to tell yambo to construct the BSE <code>(-o b)</code> , to calculate the static screened interaction <code>(-b)</code>, and to diagonalize the BS matrix <code>(-y d)</code>, as well as activate a higher verbosity level in the input file <code>-V qp</code>:		We start by generating the input file. At the command line we have to tell yambo to construct the BSE <code>(-o b)</code> , to calculate the static screened interaction <code>(-b)</code>, and to diagonalize the BS matrix <code>(-y d)</code>, as well as activate a higher verbosity level in the input file <code>-V qp</code>:

	> yambo -o b -b -y d -V qp		> yambo -o b -b -y d -V qp -F in_BSE

	The generated input file describes our first attempt to calculate the excitonic polarization spectrum of the H chain. Let's now change the bolded values		The generated input file describes our first attempt to calculate the excitonic polarization spectrum of the H chain. Let's now change the bolded values
Line 322:		Line 327:
	To avoid this anomalous electron-electron interaction we use the Random Integration Method (<code>-c</code> option).		To avoid this anomalous electron-electron interaction we use the Random Integration Method (<code>-c</code> option).

	> yambo -r -o b -b -y d		> yambo -r -o b -b -y d -F in_BSE_RIM

	and modify the <code>RandQpts</code> and <code>RandGvec</code> variables:		and modify the <code>RandQpts</code> and <code>RandGvec</code> variables:
Line 331:		Line 336:
	Here ''RandQpts'' specifies the number of random points to use and ''RandGvec'' the number of RL components to evaluate.		Here ''RandQpts'' specifies the number of random points to use and ''RandGvec'' the number of RL components to evaluate.

	After launching ~~<code~~> $ yambo~~</code> again~~ we notice a new section in the report file ~~''r_optics_bse_em1s_bss_rim_cut''~~:		After launching

			> yambo -F in_BSE_RIM -J BSE_RIM

			we notice a new section in the report file:

	[04] Coulomb potential Random Integration (RIM)		[04] Coulomb potential Random Integration (RIM)
Line 383:		Line 392:
	# Repeat the RPA, ALDA, and BSE calculations for light polarized perpendicular to the chain axis to verify that the polarization is much smaller than in the parallel case.		# Repeat the RPA, ALDA, and BSE calculations for light polarized perpendicular to the chain axis to verify that the polarization is much smaller than in the parallel case.
	# Use ypp to plot the excitonic wave function.		# Use ypp to plot the excitonic wave function.
	# Repeat the whole tutorial for the other interatomic distances~~, whose databases are provided in the tutorial zip file~~.		# Repeat the whole tutorial for the other interatomic distances.

Marini: /* The Bethe-Salpeter Equation applied to 1D systems */

2019-11-06T11:47:36Z

The Bethe-Salpeter Equation applied to 1D systems

← Older revision		Revision as of 11:47, 6 November 2019
Line 300:		Line 300:
	and to our great surprise the polarization spectrum we obtain is completely wrong, with just a poor signal around 3eV which is nonsense:		and to our great surprise the polarization spectrum we obtain is completely wrong, with just a poor signal around 3eV which is nonsense:

	[[File:~~Chain_bse_norim_new~~.png]]		[[File:2.5_bse_no_RIM.png]]

			As you can see '''the excitonic peak has even a negative intensity'''!

	The reason of this serious failure of the BS calculation is due to the peculiar geometry of the H chain, and of corresponding BZ sampling that is strictly one dimensional. This is readily detected in any report file, like ''r_setup''		The reason of this serious failure of the BS calculation is due to the peculiar geometry of the H chain, and of corresponding BZ sampling that is strictly one dimensional. This is readily detected in any report file, like ''r_setup''

	[...]		[...]
	[02.01] K-grid lattice		[02.04] K-grid lattice
	======================~~==t~~		======================
			Compatible Grid is 1D
	Compatible Grid ~~might be~~ 1D
	B1 [rlu]= -0.01250 0.00000 0.00000		B1 [rlu]= -0.01250 0.00000 0.00000
	Grid dimensions : 80		Grid dimensions : 80
	K lattice UC volume [au]: 0.0011		K lattice UC volume [au]: 0.0011

	As a consequence the ''region'' of space assigned to each k-point is strongly compressed in one of the dimensions, like the thin slices of this picture		As a consequence the ''region'' of space assigned to each k-point is strongly compressed in one of the dimensions, like the thin slices of this picture

	[[File:Chain_slices.~~png\|x65px~~]]		[[File:Chain_slices.jpg]]

	The drastic consequence of this compression is that each region receives a piece of the electron-electron interaction that is multiplied by a ''form factor'' of the region, that, in general '''is assumed spatially constant'''. With such a severe sampling of the BZ this assumption is no longer valid and the screened interaction is anomalously enhanced.		The drastic consequence of this compression is that each region receives a piece of the electron-electron interaction that is multiplied by a ''form factor'' of the region, that, in general '''is assumed spatially constant'''. With such a severe sampling of the BZ this assumption is no longer valid and the screened interaction is anomalously enhanced.

	To avoid this anomalous electron-electron interaction we use the Random Integration Method (<code>-c</code> option).		To avoid this anomalous electron-electron interaction we use the Random Integration Method (<code>-c</code> option).
	yambo -c -o b -b -y d
			> yambo -r -o b -b -y d

	and modify the <code>RandQpts</code> and <code>RandGvec</code> variables:		and modify the <code>RandQpts</code> and <code>RandGvec</code> variables:

	RandQpts= 1000000 # [RIM] Number of random q-points in the BZ		RandQpts= 1000000 # [RIM] Number of random q-points in the BZ
	RandGvec= 1 RL # [RIM] Coulomb interaction RS components		RandGvec= 1 RL # [RIM] Coulomb interaction RS components

	Here ''RandQpts'' specifies the number of random points to use and ''RandGvec'' the number of RL components to evaluate.		Here ''RandQpts'' specifies the number of random points to use and ''RandGvec'' the number of RL components to evaluate.

	After launching <code> $ yambo</code> again we notice a new section in the report file ''r_optics_bse_em1s_bss_rim_cut'':		After launching <code> $ yambo</code> again we notice a new section in the report file ''r_optics_bse_em1s_bss_rim_cut'':
	~~<pre>~~
	[04] Coulomb potential Random Integration (RIM)		[04] Coulomb potential Random Integration (RIM)
	=========		=========
Line 365:		Line 371:
	Q [39]: 0.663225 0.981867 * Q [40]: 0.680678 0.983004		Q [39]: 0.663225 0.981867 * Q [40]: 0.680678 0.983004
	Q [41]: 0.698132 0.984061		Q [41]: 0.698132 0.984061
	~~</pre>~~
	The interesting result is that the 2<sup>nd</sup> and the 4<sup>th</sup> columns of numbers reflect the effect of the BZ compression: 1 means little effect, small numbers mean large effect. We see that the effect is huge for points in the BZ with small modulus (1<sup>st</sup> and 3<sup>rd</sup> columns).		The interesting result is that the 2<sup>nd</sup> and the 4<sup>th</sup> columns of numbers reflect the effect of the BZ compression: 1 means little effect, small numbers mean large effect. We see that the effect is huge for points in the BZ with small modulus (1<sup>st</sup> and 3<sup>rd</sup> columns).

	The final BS polarizability is, now, physically correct and substantially different from ALDA:<br>		The final BS polarizability is, now, physically correct and substantially different from ALDA:<br>

	[[File:Chain_bse_rim.png\|512x384px]]		[[File:Chain_bse_rim.png\|512x384px]]

Marini: /* The Bethe-Salpeter Equation applied to 1D systems */

2019-11-06T11:34:37Z

The Bethe-Salpeter Equation applied to 1D systems

← Older revision		Revision as of 11:34, 6 November 2019
Line 250:		Line 250:
	This property causes some tricky numerical problems that are, however, related to a precise physical process: the extreme confinement of 3D electrons in a small region of space.		This property causes some tricky numerical problems that are, however, related to a precise physical process: the extreme confinement of 3D electrons in a small region of space.
	If we use yambo to perform a BS calculation you will immediately see where the problem is!		If we use yambo to perform a BS calculation you will immediately see where the problem is!

			'''Let's move in the 2.5 folder'''

			>cd YAMBO_TUTORIALS/Hydrogen_Chain/YAMBO/2.5

	We start by generating the input file. At the command line we have to tell yambo to construct the BSE <code>(-o b)</code> , to calculate the static screened interaction <code>(-b)</code>, and to diagonalize the BS matrix <code>(-y d)</code>, as well as activate a higher verbosity level in the input file <code>-V qp</code>:		We start by generating the input file. At the command line we have to tell yambo to construct the BSE <code>(-o b)</code> , to calculate the static screened interaction <code>(-b)</code>, and to diagonalize the BS matrix <code>(-y d)</code>, as well as activate a higher verbosity level in the input file <code>-V qp</code>:
	~~$ yambo -o b -b -y d -V qp~~
	~~The generated input file describes our first attempt to calculate the excitonic polarization spectrum of the H chain:~~

	~~optics # [R OPT] Optics~~		> yambo -o b -b -y d -V qp
	~~bse # [R BSK] Bethe Salpeter Equation~~.
	~~em1s # [R Xs] Static Inverse Dielectric Matrix~~		The generated input file describes our first attempt to calculate the excitonic polarization spectrum of the H chain. Let's now change the bolded values
	~~bss # [R BSS] Bethe Salpeter Equation solver~~
	~~Chimod= "Hartree" # [X] IP/Hartree/ALDA/LRC/BSfxc~~
	BSEmod= '''"causal"''' # [BSE] resonant/causal/coupling		BSEmod= '''"causal"''' # [BSE] resonant/causal/coupling
	~~BSKmod= "SEX" # [BSE] IP/Hartree/HF/ALDA/SEX/BSfxc~~
	~~BSSmod= "d" # [BSS] (h)aydock/(d)iagonalization/(i)nversion/(t)ddft`~~
	~~KfnQPdb= "none" # [EXTQP BSK BSS] Database~~
	~~KfnQP_N= 1 # [EXTQP BSK BSS] Interpolation neighbours~~
	~~% KfnQP_E~~
	~~0.000000 \| 1.000000 \| 1.000000 \| # [EXTQP BSK BSS] E parameters (c/v)~~
	%
	~~% KfnQP_W~~
	~~0.000 \| 0.000 \| 0.000 \| 0.000 \| # [EXTQP BSK BSS] W parameters (c/v)~~
	%
	~~KfnQP_Z= ( 1.000000 , 0.000000 ) # [EXTQP BSK BSS] Z factor (c/v)~~
	~~BSresKmod= "xc" # [BSK] Resonant Kernel mode. (`x`;`c`;`d`)~~
	~~% BSEBands~~
	~~1 \| 2 \| # [BSK] Bands range~~
	%
	'''BSENGBlk= 1''' RL # [BSK] Screened interaction block size		'''BSENGBlk= 1''' RL # [BSK] Screened interaction block size
	BSENGexx= '''7659''' RL # [BSK] Exchange components		BSENGexx= '''7659''' RL # [BSK] Exchange components
	~~XfnQPdb= "none" # [EXTQP Xd] Database~~
	~~XfnQP_N= 1 # [EXTQP Xd] Interpolation neighbours~~
	~~% XfnQP_E~~
	~~0.000000 \| 1.000000 \| 1.000000 \| # [EXTQP Xd] E parameters (c/v)~~
	%
	~~% XfnQP_W~~
	~~0.000 \| 0.000 \| 0.000 \| 0.000 \| # [EXTQP Xd] W parameters (c/v)~~
	%
	~~XfnQP_Z= ( 1.000000 , 0.000000 ) # [EXTQP Xd] Z factor (c/v)~~
	~~% QpntsRXs~~
	~~1 \| 41 \| # [Xs] Transferred momenta~~
	%
	% BndsRnXs		% BndsRnXs
	1 \| '''20''' \| # [BSK] Bands range		1 \| '''20''' \| # [BSK] Bands range
	%		%
	'''NGsBlkXs= 1''' RL # [Xs] Response block size		'''NGsBlkXs= 1''' RL # [Xs] Response block size
	~~% LongDrXs~~
	~~1.000000 \| 0.000000 \| 0.000000 \| # [Xs] [cc] Electric Field~~
	%
	~~BSSmod= "d" # [BSS] Solvers `h/d/i/t`~~
	~~% BEnRange~~
	~~0.00000 \| 10.00000 \| eV # [BSS] Energy range~~
	%
	~~% BDmRange~~
	~~0.10000 \| 0.10000 \| eV # [BSS] Damping range~~
	%
	~~BEnSteps= 100 # [BSS] Energy steps~~
	~~% BLongDir~~
	~~1.000000 \| 0.000000 \| 0.000000 \| # [BSS] [cc] Electric Field~~
	%
	~~Now change the highlighted values.~~
	First we consider only the resonant part of the BS equation:		First we consider only the resonant part of the BS equation:
	BSEmod= "resonant"		BSEmod= "resonant"

	Second, include a QP gap correction of 3.5 eV		Second, include a QP gap correction of 3.5 eV
	% KfnQP_E		% KfnQP_E
	3.50000 \| 1.000000 \| 1.000000 \| # [EXTQP BSK BSS] E parameters (c/v)		3.50000 \| 1.000000 \| 1.000000 \| # [EXTQP BSK BSS] E parameters (c/v)
	%		%

	Third, decide some reasonable size of the inverse dielectric function that defines the statically screened interaction (normally this has to be determined by convergence studies):		Third, decide some reasonable size of the inverse dielectric function that defines the statically screened interaction (normally this has to be determined by convergence studies):
	NGsBlkXs= 111		NGsBlkXs= 111
	BSENGexx= 111		BSENGexx= 111

	Fourth, you should change the BSE and polarization function band ranges:		Fourth, you should change the BSE and polarization function band ranges:
	% BSEBands		% BSEBands
Line 325:		Line 289:
	1 \| 2 \| # [Xs] Polarization function bands		1 \| 2 \| # [Xs] Polarization function bands
	%		%

	Two bands are enough in this case to get reasonable results.		Two bands are enough in this case to get reasonable results.

	Remember also to uncomment the variable <code>WRbsWF</code> if you want to plot the excitonic wave function afterwords.		Remember also to uncomment the variable <code>WRbsWF</code> if you want to plot the excitonic wave function afterwords.

	Finally, we launch yambo		Finally, we launch yambo
	yambo
			> yambo -J BSE

	and to our great surprise the polarization spectrum we obtain is completely wrong, with just a poor signal around 3eV which is nonsense:		and to our great surprise the polarization spectrum we obtain is completely wrong, with just a poor signal around 3eV which is nonsense:

	[[File:~~Chain_bse_norim~~.png]]		[[File:Chain_bse_norim_new.png]]

	The reason of this serious failure of the BS calculation is due to the peculiar geometry of the H chain, and of corresponding BZ sampling that is strictly one dimensional. This is readily detected in any report file, like ''r_setup''		The reason of this serious failure of the BS calculation is due to the peculiar geometry of the H chain, and of corresponding BZ sampling that is strictly one dimensional. This is readily detected in any report file, like ''r_setup''

	~~<pre>~~ [...]		[...]
	[02.01] K-grid lattice		[02.01] K-grid lattice
	====		========================t

	Compatible Grid might be 1D		Compatible Grid might be 1D
	B1 [rlu]= -0.01250 0.00000 0.00000		B1 [rlu]= -0.01250 0.00000 0.00000
	Grid dimensions : 80		Grid dimensions : 80
	K lattice UC volume [au]: 0.0011 ~~</pre>~~		K lattice UC volume [au]: 0.0011

	As a consequence the ''region'' of space assigned to each k-point is strongly compressed in one of the dimensions, like the thin slices of this picture		As a consequence the ''region'' of space assigned to each k-point is strongly compressed in one of the dimensions, like the thin slices of this picture

Marini: /* A long-range kernel beyond the TDLDA */

2019-11-06T09:46:59Z

A long-range kernel beyond the TDLDA

Marini: /* The TDLDA excitations wavefunction */

2019-11-06T09:33:04Z

The TDLDA excitations wavefunction

← Older revision		Revision as of 09:33, 6 November 2019
Line 167:		Line 167:

	Remember that the first field '''must be set to the interatomic distance divided by two'''. In the case of 2.5 a.u. the first field will be 1.25.<br />		Remember that the first field '''must be set to the interatomic distance divided by two'''. In the case of 2.5 a.u. the first field will be 1.25.<br />
	If we run now ypp ~~it will create the file ''o.exc_3d_1.xsf'' that you can plot by using~~		If we run now ypp

	> launch_xcrysden.sh o.~~density_2d~~.xsf		> ypp -F in_tdlda_density -J ALDA

			it will create the file ''o-ALDA.exc_3d_1.xsf'' that you can plot by using

			> launch_xcrysden.sh o-ALDA.exc_3d_1.xsf

	If we compare the plot with the one obtained by solving the BS equation we should see		If we compare the plot with the one obtained by solving the BS equation we should see

Marini: /* The TDLDA excitations wavefunction */

2019-11-06T09:20:39Z

The TDLDA excitations wavefunction

← Older revision		Revision as of 09:20, 6 November 2019
Line 139:		Line 139:
	We see that the peak with energy 3.78 dominates the spectra and it corresponds to the index 1. If we type now		We see that the peak with energy 3.78 dominates the spectra and it corresponds to the index 1. If we type now

	> ypp -e w		> ypp -e w -F in_tdlda_density

	to get the input file		to get the input file

Marini: /* A closer look: analysis of the electronic states */

2019-11-06T09:08:05Z

A closer look: analysis of the electronic states

← Older revision		Revision as of 09:08, 6 November 2019
Line 93:		Line 93:
	> ypp -s d		> ypp -s d
	The input file ''ypp.in'' will be		The input file ''ypp.in'' will be
	~~density~~ # [R] ~~Density~~
	~~electrons~~ # [R] ~~Electrons (and holes)~~		electrons # [R] Electrons (and holes)
	Format= ~~"~~g~~"~~ # Output format [(g)nuplot/(x)crysden]		density # [R] Density
	~~'''~~Direction= ~~"~~1~~"'''~~ # [rlu] [1/2/3] for 1d or [12/13/23] for 2d [123] for 3D		Format= "g" # Output format [(c)ube/(g)nuplot/(x)crysden]
	FFTGvecs= 7659 RL # [FFT] Plane-waves		Direction= "1" # [rlu] [1/2/3] for 1d or [12/13/23] for 2d [123] for 3D
			FFTGvecs= 7659 RL # [FFT] Plane-waves


	As our system is one-dimensional and it is lying parallel to the z axis we need to change to ''Direction="12"'' so to perform a contour plot on the "XY" plane.		As our system is one-dimensional and it is lying parallel to the z axis we need to change to ''Direction="12"'' so to perform a contour plot on the "XY" plane.
	To use XCrysden switch to "x" the value of the ''Format'' variable.<br />		To use XCrysden switch to "x" the value of the ''Format'' variable.<br />
	Now you can launch ypp.		Now you can launch ypp.
	$ ypp
	At the end of the quick calculation you will find in your directory the file ''o.density_2d.xsf'' that you can plot using Xcrysden. You can view the density directly using the script ~~provided in the ''../bin/'' folder~~. To use it type:		> ypp
	~~$../bin/~~launch_xcrysden.sh o.density_2d.xsf
			At the end of the quick calculation you will find in your directory the file ''o.density_2d.xsf'' that you can plot using Xcrysden.

			You can view the density directly using the [[Bash_scripts\|launch_xcrysden.sh]] shell script. To use it type:

			>launch_xcrysden.sh o.density_2d.xsf

	Follow the same procedure for the other distance and compare the two densities. You should see something like		Follow the same procedure for the other distance and compare the two densities. You should see something like

	~~<!-- [[File:Chain 2.05 structure.png\|x50px]][[File:Chain_2.05.o.density_2d.xsf.png\|x50px]]<br>~~
	~~[[File:Chain_2.5.png\|x50px]][[File:Chain_2.5.o.density_2d.xsf.png\|x50px]]<br> -->~~

	[[File:Chain 2.05 structure.png\|300px]] [[File:Chain_2.5.png\|300px]] <br>		[[File:Chain 2.05 structure.png\|300px]] [[File:Chain_2.5.png\|300px]] <br>
Line 120:		Line 125:
	A mean large distance between the electron and hole also reflects the poor correlation felt by the two bodies. YPP can plot either the case where the electron and the hole are forced to be in the same space point, or the case where the hole's position is fixed somewhere and the electron is left free to move. This second case is more appropriate here.<br />		A mean large distance between the electron and hole also reflects the poor correlation felt by the two bodies. YPP can plot either the case where the electron and the hole are forced to be in the same space point, or the case where the hole's position is fixed somewhere and the electron is left free to move. This second case is more appropriate here.<br />
	We need first to identify the index of the corresponding eigenstate. Running		We need first to identify the index of the corresponding eigenstate. Running
	$ ypp -e s
	YPP will create a file named ''o.exc_I_sorted'' that contains the list of peaks in the dielectric function ordered with increasing peak intensity.		> ypp -e s -J ALDA
	~~<pre>~~#
	# E [ev] Strength Index		YPP will create a file named ''o-ALDA.exc_I_sorted'' that contains the list of peaks in the dielectric function ordered with increasing peak intensity.
	#
			#
			# E [ev] Strength Index
			#
	3.783688 1.000000 1.000000		3.783688 1.000000 1.000000
	4.38457 0.03179 3.00000		4.38457 0.03179 3.00000
	5.171 0.3731E-2 5.000<~~/pre>~~		5.171 0.3731E-2 5.000<

	We see that the peak with energy 3.78 dominates the spectra and it corresponds to the index 1. If we type now		We see that the peak with energy 3.78 dominates the spectra and it corresponds to the index 1. If we type now
	$ ypp -e w
			> ypp -e w

	to get the input file		to get the input file

	exc_wf # [R] Excitonic Wavefunction		exc_wf # [R] Excitonic Wavefunction
	excp # [R] Excitonic Properties		excp # [R] Excitonic Properties
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	0.000 \| 0.000 \| 0.000 \| # [cc] Hole position in unit cell		0.000 \| 0.000 \| 0.000 \| # [cc] Hole position in unit cell
	%		%

	It is interesting to do a 3D plot. To this end we set ''Direction="123"'' and replace the first component in Cells with 16 (this value will expand the unit cell along the X direction). The ''States'' variable is already set to the peak number 1.<br />		It is interesting to do a 3D plot. To this end we set ''Direction="123"'' and replace the first component in Cells with 16 (this value will expand the unit cell along the X direction). The ''States'' variable is already set to the peak number 1.<br />

	We put the hole in the middle of the chain by setting		We put the hole in the middle of the chain by setting

	% Hole		% Hole
	1.02500 \| 12.50000 \| 12.50000 \| # [cc] Hole position in unit ce		1.02500 \| 12.50000 \| 12.50000 \| # [cc] Hole position in unit ce
	%		%

	Remember that the first field '''must be set to the interatomic distance divided by two'''. In the case of 2.5 a.u. the first field will be 1.25.<br />		Remember that the first field '''must be set to the interatomic distance divided by two'''. In the case of 2.5 a.u. the first field will be 1.25.<br />
	If we run now ypp it will create the file ''o.exc_3d_1.xsf'' that you can plot by using		If we run now ypp it will create the file ''o.exc_3d_1.xsf'' that you can plot by using
	~~$ ../bin/~~launch_xcrysden.sh o.density_2d.xsf
			> launch_xcrysden.sh o.density_2d.xsf

	If we compare the plot with the one obtained by solving the BS equation we should see		If we compare the plot with the one obtained by solving the BS equation we should see

	{\| class="wikitable" style="text-align: center;		{\| class="wikitable" style="text-align: center;
	\|colspan="2"\|'''Excitation wavefunctions for 2.05 a.u. distance'''		\|colspan="2"\|'''Excitation wavefunctions for 2.05 a.u. distance'''

Marini: /* The electronic density */

2019-11-06T08:36:38Z

The electronic density

← Older revision		Revision as of 08:36, 6 November 2019
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	To this end we can use the yambo post/pre processor (YPP). <code>ypp</code> is capable of performing some basic analyses using the pre-calculated informations stored in the yambo databases.<br />		To this end we can use the yambo post/pre processor (YPP). <code>ypp</code> is capable of performing some basic analyses using the pre-calculated informations stored in the yambo databases.<br />
	YPP works like yambo. It uses a series of options to create an input file containing only the variables that are relevant to that type of calculation. Launch it with the help (-H) flag to see a full list of options.		YPP works like yambo. It uses a series of options to create an input file containing only the variables that are relevant to that type of calculation. Launch it with the help (-H) flag to see a full list of options.
	$ cd 2.05/		> cd 2.05/
	$ ypp -H		> ypp -H

	To plot the density we need to type		To plot the density we need to type
	ypp -p d		> ypp -s d
	The input file ''ypp.in'' will be		The input file ''ypp.in'' will be
	density # [R] Density		density # [R] Density

← Older revision		Revision as of 09:46, 6 November 2019
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	The key point is to realize that, indeed, the f<sub>xc</sub> kernel acts like a self-energy in the Dyson equation for χ. As in the case of quasiparticles, the most optimal self-energy can be chosen by looking at the structure of the bare propagator, χ<sub>0</sub> in this case.<br />		The key point is to realize that, indeed, the f<sub>xc</sub> kernel acts like a self-energy in the Dyson equation for χ. As in the case of quasiparticles, the most optimal self-energy can be chosen by looking at the structure of the bare propagator, χ<sub>0</sub> in this case.<br />
	In the long wavelength limit χ<sub>0</sub> behaves like q<sup>2</sup>. As a naive consequence the self-energy must cancel this power dependence to ensure that the product f<sub>xc</sub>χ<sub>0</sub> remains finite in the optical limit.		In the long wavelength limit χ<sub>0</sub> behaves like q<sup>2</sup>. As a naive consequence the self-energy must cancel this power dependence to ensure that the product f<sub>xc</sub>χ<sub>0</sub> remains finite in the optical limit.

	This simple argument is enough to introduce the long-range TDDFT kernel:<br>		This simple argument is enough to introduce the long-range TDDFT kernel:<br>

	[[File:Chain_PIC_doc_TDDFT-129.png]] <br>		[[File:Chain_PIC_doc_TDDFT-129.png]] <br>

	Now we will use this kernel with a static approximation for the parameter alpha, first for the chain of intermolecular distance 2.5 a.u..		Now we will use this kernel with a static approximation for the parameter alpha, first for the chain of intermolecular distance 2.5 a.u..
	Enter the 2.5 directory and generate the input file for a TDDFT calculation in reciprocal space, specifying you want the long-range kernel:		Enter the 2.5 directory and generate the input file for a TDDFT calculation in reciprocal space, specifying you want the long-range kernel:
	$ cd 2.5
	$ yambo -o c -~~t l~~		> cd 2.5
			> yambo -o c -k lrc

	Change the highlighted variables in the input file:		Change the highlighted variables in the input file:

	Chimod= "LRC" # [X] IP/Hartree/ALDA/LRC/BSfxc		Chimod= "LRC" # [X] IP/Hartree/ALDA/LRC/BSfxc
	LRC_alpha= '''0.000000''' # [TDDFT] LRC alpha factor		LRC_alpha= '''0.000000''' # [TDDFT] LRC alpha factor
Line 226:		Line 232:
	NGsBlkXd= '''100''' RL # [Xd] Response block size (Put some local fields, not too much)		NGsBlkXd= '''100''' RL # [Xd] Response block size (Put some local fields, not too much)
	ETStpsXd= '''1000''' # [Xd] Total Energy steps		ETStpsXd= '''1000''' # [Xd] Total Energy steps

	and run yambo. Now we can perform different calculations assigning different values to the variable LRC_alpha. This value is a static approximation to α(ω) in the long-range expression for f<sub>xc</sub>. This must be negative (the interaction between electron and hole is attractive). Try different numbers in the range 0 to -20. You will see that around <code>LRC_alpha=-19</code> we obtain the same excitation energy of the BSE spectrum:<br>		and run yambo. Now we can perform different calculations assigning different values to the variable LRC_alpha. This value is a static approximation to α(ω) in the long-range expression for f<sub>xc</sub>. This must be negative (the interaction between electron and hole is attractive). Try different numbers in the range 0 to -20. You will see that around <code>LRC_alpha=-19</code> we obtain the same excitation energy of the BSE spectrum:<br>

	[[File:Chain lrc.png]] <br>		[[File:Chain lrc.png]] <br>

	Now you can repeat the same calculations for the chain with 2.05 intermolecular distance. Once you will find the optimal value of %alpha, you will realize that as expected, it is one order of magnitude smaller than the one needed for the previous, more inhomogeneous system.		Now you can repeat the same calculations for the chain with 2.05 intermolecular distance. Once you will find the optimal value of %alpha, you will realize that as expected, it is one order of magnitude smaller than the one needed for the previous, more inhomogeneous system.

	[[File:Chain lrc 2.png]] <br>		[[File:Chain lrc 2.png]] <br>

	To conclude this tutorial note that the value of &alpha you found is much larger then in any solid, as showed in this picture. Can you understand why? <br />		To conclude this tutorial note that the value of &alpha you found is much larger then in any solid, as showed in this picture. Can you understand why? <br />

	[[File:Chain alpha.png]]		[[File:Chain alpha.png]]