Solution LAB2 guanine 4 - Revision history

Daniele Varsano at 08:24, 1 April 2021

2021-04-01T08:24:18Z

← Older revision		Revision as of 08:24, 1 April 2021
Line 55:		Line 55:
	that can be plotted:		that can be plotted:

	[[File:pdos_guanine.png\|none\|~~300px~~\|top\|]]		[[File:pdos_guanine.png\|none\|400px\|top\|]]

	note the energy reference can be found in the quantum espresso output and here you can recognise the peaks corresponding to HOMO and LUMO at -5.42 and -1.37 eV.		note the energy reference can be found in the quantum espresso output and here you can recognise the peaks corresponding to HOMO and LUMO at -5.42 and -1.37 eV.

Daniele Varsano at 08:22, 1 April 2021

2021-04-01T08:22:32Z

← Older revision		Revision as of 08:22, 1 April 2021
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	sumpdos.x guanine_DFT.pdos_O > O.dat		sumpdos.x guanine_DFT.pdos_O > O.dat
	sumpdos.x guanine_DFT.pdos_H > H.dat		sumpdos.x guanine_DFT.pdos_H > H.dat

			that can be plotted:

			[[File:pdos_guanine.png\|none\|300px\|top\|]]

			note the energy reference can be found in the quantum espresso output and here you can recognise the peaks corresponding to HOMO and LUMO at -5.42 and -1.37 eV.

Daniele Varsano at 08:14, 1 April 2021

2021-04-01T08:14:17Z

← Older revision		Revision as of 08:14, 1 April 2021
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	guanine_DFT.pdos_atm#8(N)_wfc#2(p) contains the dos projected on the p orbitals of the eighth Nitrogen atom		guanine_DFT.pdos_atm#8(N)_wfc#2(p) contains the dos projected on the p orbitals of the eighth Nitrogen atom

			The projected dos can be further processed. To obtain the projected dos on a species we can sum up the DOS on all the atoms of the same species using the <code>sumpdos.x</code> executable e.g.:

			sumpdos.x guanine_DFT.pdos_C > C.dat
			sumpdos.x guanine_DFT.pdos_N > N.dat
			sumpdos.x guanine_DFT.pdos_O > O.dat
			sumpdos.x guanine_DFT.pdos_H > H.dat

Daniele Varsano at 08:04, 1 April 2021

2021-04-01T08:04:57Z

← Older revision		Revision as of 08:04, 1 April 2021
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	guanine_DFT.pdos_atm#1(C)_wfc#1(s) contains the dos projected on the s orbital of the first Carbon atom		guanine_DFT.pdos_atm#1(C)_wfc#1(s) contains the dos projected on the s orbital of the first Carbon atom

	~~guanine~~.pdos_atm#8(N)_wfc#2(p) contains the dos projected on the p orbitals of the eighth Nitrogen atom		guanine_DFT.pdos_atm#8(N)_wfc#2(p) contains the dos projected on the p orbitals of the eighth Nitrogen atom

Daniele Varsano at 08:04, 1 April 2021

2021-04-01T08:04:44Z

← Older revision		Revision as of 08:04, 1 April 2021
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	it produces a file containing the total density of states (guanine_DFT.pdos_tot) and a series of files containing the density of states projected on each atom and each atomic orbital e.g.		it produces a file containing the total density of states (guanine_DFT.pdos_tot) and a series of files containing the density of states projected on each atom and each atomic orbital e.g.

	guanine_DFT.pdos_atm#1(C)_wfc#1(s) contains the dos projected on the s orbital of the first Carbon atom		guanine_DFT.pdos_atm#1(C)_wfc#1(s) contains the dos projected on the s orbital of the first Carbon atom

	guanine.pdos_atm#8(N)_wfc#2(p) contains the dos projected on the p orbitals of the eighth Nitrogen atom		guanine.pdos_atm#8(N)_wfc#2(p) contains the dos projected on the p orbitals of the eighth Nitrogen atom

Daniele Varsano at 08:04, 1 April 2021

2021-04-01T08:04:29Z

← Older revision		Revision as of 08:04, 1 April 2021
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	Here is a sketch of the guanine HOMO isosurface:		Here is a sketch of the guanine HOMO isosurface:
	[[File:Guanine HOMO.png\|none\|300px\|top\|]]		[[File:Guanine HOMO.png\|none\|300px\|top\|]]

			* Total and projected density of states are calculated using <code>projwfc.x</code>. An example of input file is:
			&PROJWFC
			prefix='guanine_DFT'
			outdir="./SCRATCH"
			ngauss=0
			degauss=0.01
			/

			by running as
			projwfc.x < pdos.in > pdos.out

			it produces a file containing the total density of states (guanine_DFT.pdos_tot) and a series of files containing the density of states projected on each atom and each atomic orbital e.g.
			guanine_DFT.pdos_atm#1(C)_wfc#1(s) contains the dos projected on the s orbital of the first Carbon atom
			guanine.pdos_atm#8(N)_wfc#2(p) contains the dos projected on the p orbitals of the eighth Nitrogen atom

Andrea Ferretti at 11:18, 26 March 2021

2021-03-26T11:18:47Z

← Older revision		Revision as of 11:18, 26 March 2021
Line 27:		Line 27:

	Here is a sketch of the guanine HOMO isosurface:		Here is a sketch of the guanine HOMO isosurface:
	[[File:Guanine HOMO.png\|none\|~~400px~~\|top\|]]		[[File:Guanine HOMO.png\|none\|300px\|top\|]]

Andrea Ferretti at 11:18, 26 March 2021

2021-03-26T11:18:35Z

← Older revision		Revision as of 11:18, 26 March 2021
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	should produce as output the file <code>wfc_HOMO.xsf</code> that can be plotted using <code>xcrysden</code>.		should produce as output the file <code>wfc_HOMO.xsf</code> that can be plotted using <code>xcrysden</code>.

			Here is a sketch of the guanine HOMO isosurface:
			[[File:Guanine HOMO.png\|none\|400px\|top\|]]

Andrea Ferretti: Created page with " * Back to the previous page: Electronic properties of isolated molecules#Exercise 4 An example of input file for `pp.x` to plot the HOMO of guanine (pp_HOMO.i..."

2021-03-26T10:58:50Z

Created page with " * Back to the previous page: Electronic properties of isolated molecules#Exercise 4 An example of input file for <code>pp.x</code> to plot the HOMO of guanine (pp_HOMO.i..."

New page

* Back to the previous page: [[Electronic properties of isolated molecules#Exercise 4]]

An example of input file for <code>pp.x</code> to plot the HOMO of guanine (pp_HOMO.in) follows:

&INPUTPP
prefix="guanine_DFT"
outdir="./SCRATCH"
plot_num=7
filplot = "wfc_HOMO.pp"
kband=28
kpoint=1
lsign=.true.
/
&PLOT
nfile=1
filepp(1)="wfc_HOMO.pp"
iflag=3
output_format=5
fileout="wfc_HOMO.xsf"
/

by running as
pp.x < pp_HOMO.in > pp_HOMO.out

should produce as output the file <code>wfc_HOMO.xsf</code> that can be plotted using <code>xcrysden</code>.

Solution LAB2 guanine 4 - Revision history

Daniele Varsano at 08:24, 1 April 2021

Daniele Varsano at 08:22, 1 April 2021

Daniele Varsano at 08:14, 1 April 2021

Daniele Varsano at 08:04, 1 April 2021

Daniele Varsano at 08:04, 1 April 2021

Daniele Varsano at 08:04, 1 April 2021

Andrea Ferretti at 11:18, 26 March 2021

Andrea Ferretti at 11:18, 26 March 2021

Andrea Ferretti: Created page with " * Back to the previous page: Electronic properties of isolated molecules#Exercise 4 An example of input file for pp.x to plot the HOMO of guanine (pp_HOMO.i..."

Andrea Ferretti: Created page with " * Back to the previous page: Electronic properties of isolated molecules#Exercise 4 An example of input file for `pp.x` to plot the HOMO of guanine (pp_HOMO.i..."