Generating the Yambo databases - Revision history

Conor: Blanked the page

2017-03-23T14:53:27Z

Blanked the page

← Older revision		Revision as of 14:53, 23 March 2017
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	~~== UNDER CONSTRUCTION (CH) ==~~
	~~UNPACK IN SAME PLACE~~

	~~In this tutorial we will give a step-by-step demonstration how to generate the Yambo databases starting from a PWscf calculation.~~
	~~== Prerequisites ==~~
	~~[[File:HBN-bulk-3x3-annotated.png\|thumb\|Atomic structure of bulk hBN]]~~

	~~[[File:HBN2.png\|thumb\|Atomic structure of 2D hBN]]~~

	~~'''Material properties''':~~
	* HCP lattice, ABAB stacking
	* Four atoms per cell, B and N (16 electrons, )
	* Lattice constants: ''a'' = 4.716 [a.u.], ''c/a'' = 2.582
	* Plane wave cutoff 40 Ry (1500 RL vectors in wavefunctions)

	~~'''You will need''':~~
	* PWSCF input files and pseudopotentials for hBN bulk (Download here)
	* <code>pw.x</code> executable, version 5.0 or later
	* <code>p2y</code> executable

	~~Unpack the TARFILE:~~
	~~$ tar -xcvf hBN-bulk.tar~~
	~~$ cd hBN/PWSCF~~
	~~$ ls~~
	~~hbn_bands.in hbn_nscf.in hbn_scf.in hbn_scf_b.in REFERENCES~~

	~~== DFT calculations ==~~
	~~First run the SCF calculation in the usual manner, e.g.~~
	~~pw.x < hBN_scf.in > hBN_scf.out~~
	~~and then the non-SCF calculation to generate a set of Kohn-Sham eigenvalues and eigenvectors across a denser k-point mesh and for occupied and unoccupied states:~~
	~~pw.x < hBN_nscf.in > hBN_nscf.out~~
	~~Note the presence of the following flags in the input file:~~
	~~wf_collect=.true.~~
	~~force_symmorphic=.true.~~
	which are needed for the next step. Full explanations of these variables are given on the [http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html quantum-ESPRESSO input variables page]. After these two runs, you should have a <code>hBN.save</code> directory:
	~~$ ls hBN.save~~
	~~data-file.xml~~

	~~== Conversion to Yambo format ==~~
	~~PWscf output is converted to the Yambo format using the <code>p2y</code> (pwscf to yambo), found in the yambo <code>bin</code> directory.~~
	~~Enter the <code>hbn.save</code> directory and launch <code>p2y</code>:~~

	~~$ cd hBN.save~~
	~~$ p2y~~
	~~[output]~~

	~~The code reports some information about the system and generates a <code>SAVE</code> directory:~~
	~~$ ls~~
	~~SAVE HB,in etc~~
	~~$ ls SAVE~~
	~~ns.db1 ns.wf ns.kb_pp_pwscf~~
	~~ns.wf_fragments_1_1 ...~~
	~~ns.kb_pp_pwscf_fragment_1 ...~~

	~~Finally, let's move the SAVE directory into a new clean folder:~~
	~~mv SAVE ../YAMBO/~~

	~~== Advanced users ==~~
	~~<code>p2y<code> accepts several command line options:~~
	~~$ p2y -H~~
	~~dfadsfas~~



	~~----~~
	~~Next tutorial: [[Introduction to yambo: input, output and command line interface]]~~

Conor: /* Prerequisites */

2017-03-16T20:28:06Z

Prerequisites

← Older revision		Revision as of 20:28, 16 March 2017
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	== Prerequisites ==		== Prerequisites ==
	[[File:HBN-bulk-3x3-annotated.png\|thumb\|Atomic structure of bulk hBN]]		[[File:HBN-bulk-3x3-annotated.png\|thumb\|Atomic structure of bulk hBN]]

			[[File:HBN2.png\|thumb\|Atomic structure of 2D hBN]]

	'''Material properties''':		'''Material properties''':

Conor at 16:28, 14 March 2017

2017-03-14T16:28:45Z

← Older revision		Revision as of 16:28, 14 March 2017
Line 1:		Line 1:
	== UNDER CONSTRUCTION (CH) ==		== UNDER CONSTRUCTION (CH) ==
			UNPACK IN SAME PLACE

	In this tutorial we will give a step-by-step demonstration how to generate the Yambo databases starting from a PWscf calculation.		In this tutorial we will give a step-by-step demonstration how to generate the Yambo databases starting from a PWscf calculation.
	== Prerequisites ==		== Prerequisites ==
	~~You will need the DFT input files and pseudopotentials for bulk hexagonal BN (hBN), and a working <code>p2y</code> executable.~~
	[[File:HBN-bulk-3x3-annotated.png\|thumb\|Atomic structure of bulk hBN]]		[[File:HBN-bulk-3x3-annotated.png\|thumb\|Atomic structure of bulk hBN]]

	== ~~SCF run~~ ==		'''Material properties''':
	== ~~NSCF~~ run ==		* HCP lattice, ABAB stacking
	== ~~p2y conversion~~ ==		* Four atoms per cell, B and N (16 electrons, )
	<code>p2y</code> (~~PWscf~~ to yambo) ~~is a small code for converting data from a~~ <code>~~PREFIX.save~~</code> directory ~~into a format that can be read by Yambo~~. ~~In general, it is sufficient just to enter~~ the <code>~~PREFIX~~.save</code> directory and launch <code>p2y</code>:		* Lattice constants: ''a'' = 4.716 [a.u.], ''c/a'' = 2.582
			* Plane wave cutoff 40 Ry (1500 RL vectors in wavefunctions)

			'''You will need''':
			* PWSCF input files and pseudopotentials for hBN bulk (Download here)
			* <code>pw.x</code> executable, version 5.0 or later
			* <code>p2y</code> executable

			Unpack the TARFILE:
			$ tar -xcvf hBN-bulk.tar
			$ cd hBN/PWSCF
			$ ls
			hbn_bands.in hbn_nscf.in hbn_scf.in hbn_scf_b.in REFERENCES

			== DFT calculations ==
			First run the SCF calculation in the usual manner, e.g.
			pw.x < hBN_scf.in > hBN_scf.out
			and then the non-SCF calculation to generate a set of Kohn-Sham eigenvalues and eigenvectors across a denser k-point mesh and for occupied and unoccupied states:
			pw.x < hBN_nscf.in > hBN_nscf.out
			Note the presence of the following flags in the input file:
			wf_collect=.true.
			force_symmorphic=.true.
			which are needed for the next step. Full explanations of these variables are given on the [http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html quantum-ESPRESSO input variables page]. After these two runs, you should have a <code>hBN.save</code> directory:
			$ ls hBN.save
			data-file.xml

			== Conversion to Yambo format ==
			PWscf output is converted to the Yambo format using the <code>p2y</code> (pwscf to yambo), found in the yambo <code>bin</code> directory.
			Enter the <code>hbn.save</code> directory and launch <code>p2y</code>:

	$ cd hBN.save		$ cd hBN.save
	~~$ ls~~
	~~data-file.xml ...~~
	$ p2y		$ p2y
	[output]		[output]

			The code reports some information about the system and generates a <code>SAVE</code> directory:
	~~We start using~~ the <code>SAVE</code> ~~database created in the [[Generating the Yambo databases\|Generating the Yambo databases tutorial]] for bulk hBN. First, enter the~~ directory ~~for hBN containing the <code>SAVE</code> folder~~:		$ ls
	$ ls		SAVE HB,in etc
	SAVE
	$ ls SAVE		$ ls SAVE
	ns.db1 ns.wf ns.kb_pp_pwscf		ns.db1 ns.wf ns.kb_pp_pwscf
	ns.wf_fragments_1_1 ...		ns.wf_fragments_1_1 ...
	ns.kb_pp_pwscf_fragment_1 ...		ns.kb_pp_pwscf_fragment_1 ...
	~~Remember: do not try to run yambo from ''inside'~~' the <code>~~SAVE~~</code> ~~folder!~~
			Finally, let's move the SAVE directory into a new clean folder:
			mv SAVE ../YAMBO/

			== Advanced users ==
			<code>p2y<code> accepts several command line options:
			$ p2y -H
			dfadsfas



	----		----
	Next tutorial: [Introduction to yambo: input, output and command line interface]		Next tutorial: [[Introduction to yambo: input, output and command line interface]]

Conor at 15:01, 14 March 2017

2017-03-14T15:01:22Z

← Older revision		Revision as of 15:01, 14 March 2017
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			== UNDER CONSTRUCTION (CH) ==

	In this tutorial we will give a step-by-step demonstration how to generate the Yambo databases starting from a PWscf calculation.		In this tutorial we will give a step-by-step demonstration how to generate the Yambo databases starting from a PWscf calculation.
	== Prerequisites ==		== Prerequisites ==

Conor at 14:40, 14 March 2017

2017-03-14T14:40:24Z

← Older revision		Revision as of 14:40, 14 March 2017
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	ns.kb_pp_pwscf_fragment_1 ...		ns.kb_pp_pwscf_fragment_1 ...
	Remember: do not try to run yambo from ''inside'' the <code>SAVE</code> folder!		Remember: do not try to run yambo from ''inside'' the <code>SAVE</code> folder!

			----
			Next tutorial: [Introduction to yambo: input, output and command line interface]

Conor: Created page with "In this tutorial we will give a step-by-step demonstration how to generate the Yambo databases starting from a PWscf calculation. == Prerequisites == You will need the DFT in..."

2017-03-14T14:37:35Z

Created page with "In this tutorial we will give a step-by-step demonstration how to generate the Yambo databases starting from a PWscf calculation. == Prerequisites == You will need the DFT in..."

New page

In this tutorial we will give a step-by-step demonstration how to generate the Yambo databases starting from a PWscf calculation.
== Prerequisites ==
You will need the DFT input files and pseudopotentials for bulk hexagonal BN (hBN), and a working <code>p2y</code> executable.
[[File:HBN-bulk-3x3-annotated.png|thumb|Atomic structure of bulk hBN]]

== SCF run ==
== NSCF run ==
== p2y conversion ==
<code>p2y</code> (PWscf to yambo) is a small code for converting data from a <code>PREFIX.save</code> directory into a format that can be read by Yambo. In general, it is sufficient just to enter the <code>PREFIX.save</code> directory and launch <code>p2y</code>:

$ cd hBN.save
$ ls
data-file.xml ...
$ p2y
[output]

We start using the <code>SAVE</code> database created in the [[Generating the Yambo databases|Generating the Yambo databases tutorial]] for bulk hBN. First, enter the directory for hBN containing the <code>SAVE</code> folder:
$ ls
SAVE
$ ls SAVE
ns.db1 ns.wf ns.kb_pp_pwscf
ns.wf_fragments_1_1 ...
ns.kb_pp_pwscf_fragment_1 ...
Remember: do not try to run yambo from ''inside'' the <code>SAVE</code> folder!