Input file generation - Revision history

Davide: /* Prerequisites */

2017-04-21T10:14:10Z

Prerequisites

← Older revision		Revision as of 10:14, 21 April 2017
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	== Prerequisites ==		== Prerequisites ==
	'''Previous modules'''		'''Previous modules'''
	* Initialization for [[Bulk_material:_h-BN\|bulk hBN]].		* Initialization for [[Bulk_material:_h-BN\|bulk hBN]] or [[2D_material:_h-BN_sheet\|2D hBN]]
			Below you will find all the instructions for the '''bulk hBN''' case.

	'''You will need''':		'''You will need''':

Davide at 09:52, 21 April 2017

2017-04-21T09:52:32Z

← Older revision		Revision as of 09:52, 21 April 2017
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	The input file generator of Yambo is thus an ''intelligent'' parser, which interacts with the user and the existing databases. For this reason we recommend that you always use Yambo to generate the input files, rather than making them yourself.		The input file generator of Yambo is thus an ''intelligent'' parser, which interacts with the user and the existing databases. For this reason we recommend that you always use Yambo to generate the input files, rather than making them yourself.

	~~== Links ==~~
	* Next module: [[Command_line_options\|Command line options]]
	* Back to [[First steps: a walk through from DFT to optical properties\|First steps with yambo]] tutorial
	* [[Tutorials\|Back to tutorials menu]]

	<br>		<br>
	{\| style="width:100%" border="1"		{\| style="width:100%" border="1"
	\|style="width:15%; text-align:left"\|Prev: [[~~Bulk_material:_h-BN~~\|~~bulk hBN~~]]		\|style="width:15%; text-align:left"\|Prev: [[Initialization\|Initialization]]
	\|style="width:70%; text-align:center"\|Now: [[Tutorials\|Tutorials Home]] --> [[First_steps:_a_walk_through_from_DFT_to_optical_properties\|First steps]] --> [[Bulk_material:_h-BN\|bulk hBN]] --> [[~~Initialization~~\|~~Initialization~~]]		\|style="width:70%; text-align:center"\|Now: [[Tutorials\|Tutorials Home]] --> [[First_steps:_a_walk_through_from_DFT_to_optical_properties\|First steps]] --> [[Bulk_material:_h-BN\|bulk hBN]] / [[2D_material:_h-BN_sheet\|2D hBN]] --> [[Input_file_generation\|Input file]]
	\|style="width:15%; text-align:right"\|Next: [[Command_line_options\|Command line options]]		\|style="width:15%; text-align:right"\|Next: [[Command_line_options\|Command line options]]
	\|-		\|-
	\|}		\|}

Davide at 09:48, 21 April 2017

2017-04-21T09:48:02Z

← Older revision		Revision as of 09:48, 21 April 2017
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	* Back to [[First steps: a walk through from DFT to optical properties\|First steps with yambo]] tutorial		* Back to [[First steps: a walk through from DFT to optical properties\|First steps with yambo]] tutorial
	* [[Tutorials\|Back to tutorials menu]]		* [[Tutorials\|Back to tutorials menu]]

			<br>
			{\| style="width:100%" border="1"
			\|style="width:15%; text-align:left"\|Prev: [[Bulk_material:_h-BN\|bulk hBN]]
			\|style="width:70%; text-align:center"\|Now: [[Tutorials\|Tutorials Home]] --> [[First_steps:_a_walk_through_from_DFT_to_optical_properties\|First steps]] --> [[Bulk_material:_h-BN\|bulk hBN]] --> [[Initialization\|Initialization]]
			\|style="width:15%; text-align:right"\|Next: [[Command_line_options\|Command line options]]
			\|-
			\|}

Conor: /* Changing input parameters */

2017-03-30T17:24:14Z

Changing input parameters

← Older revision		Revision as of 17:24, 30 March 2017
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	This indicates that Yambo has read the new input value (1000 G-vectors), checked the database of G-vector shells ''(SAVE/ndb.gops)'',		This indicates that Yambo has read the new input value (1000 G-vectors), checked the database of G-vector shells ''(SAVE/ndb.gops)'',
	and changed the input value to one that fits a completely closed shell.		and changed the input value to one that fits a completely closed shell.

			Last, note that Yambo variables can be expressed in different '''units'''. In this case, <code>RL</code> can be replaced by an energy unit like Ry, eV, Ha, etc. Energy units are generally better as they are independent of the cell size. Technical information is available on the [[Variables]] page.

	The input file generator of Yambo is thus an ''intelligent'' parser, which interacts with the user and the existing databases. For this reason we recommend that you always use Yambo to generate the input files, rather than making them yourself.		The input file generator of Yambo is thus an ''intelligent'' parser, which interacts with the user and the existing databases. For this reason we recommend that you always use Yambo to generate the input files, rather than making them yourself.

Conor at 16:31, 30 March 2017

2017-03-30T16:31:55Z

← Older revision		Revision as of 16:31, 30 March 2017
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	In this ~~tutorial~~ you will learn how to generate and modify an input file with Yambo.		In this module you will learn how to generate and modify an input file with Yambo.

	== Prerequisites ==		== Prerequisites ==

Conor at 16:11, 30 March 2017

2017-03-30T16:11:49Z

← Older revision		Revision as of 16:11, 30 March 2017
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	'''You will need''':		'''You will need''':
	* The <code>SAVE</code> databases for bulk hBN ~~('''Download here''')~~		* The <code>SAVE</code> databases for bulk hBN
	* The <code>yambo</code> executable		* The <code>yambo</code> executable

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	==Combining options==		==Combining options==
	Multiple options can be used together to activate various tasks or runlevels (in some cases this is actually a necessity).		Multiple options can be used together to activate various tasks or runlevels (in some cases this is actually a necessity).
	For instance, to generate an input file for optical spectra including local field effects (Hartree approximation), do		For instance, to generate an input file for optical spectra including local field effects (Hartree approximation), do (and then exit)
	$ yambo -o c -k hartree ''which switches on:''		$ yambo -o c -k hartree ''which switches on:''
	optics # [R OPT] Optics		optics # [R OPT] Optics
	chi # [R CHI] Dyson equation for Chi.		chi # [R CHI] Dyson equation for Chi.
	Chimod= "Hartree" # [X] IP/Hartree/ALDA/LRC/BSfxc		Chimod= "Hartree" # [X] IP/Hartree/ALDA/LRC/BSfxc
	To perform a Hartree-Fock and GW calculation using a plasmon-pole approximation, do:		To perform a Hartree-Fock and GW calculation using a plasmon-pole approximation, do (and then exit):
	$ yambo -x -g n -p p ''which switches on:''		$ yambo -x -g n -p p ''which switches on:''
	HF_and_locXC # [R XX] Hartree-Fock Self-energy and Vxc		HF_and_locXC # [R XX] Hartree-Fock Self-energy and Vxc
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	$ yambo -x		$ yambo -x
	Inside the generated input file you should find:		Inside the generated input file you should find:
	EXXRLvcs= 3187 RL # [XX] Exchange RL components		[[Variables#EXXRLvcs\|EXXRLvcs]] = 3187 RL # [XX] Exchange RL components
	%QPkrange # [GW] QP generalized Kpoint/Band indices		%[[Variables#QPkrange\|QPkrange]] # [GW] QP generalized Kpoint/Band indices
	1\| 14\| 1\|100\|		1\| 14\| 1\|100\|
	%		%

Conor at 14:58, 30 March 2017

2017-03-30T14:58:29Z

← Older revision		Revision as of 14:58, 30 March 2017
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	* The <code>yambo</code> executable		* The <code>yambo</code> executable

	== ~~Launch the input~~ file generator ==		== Input file generator ==
			First, move to the appropriate folder and initialize the Yambo databases if you haven't already done so.
			$ cd YAMBO_TUTORIALS/hBN/YAMBO
			$ yambo

	Yambo generates its own input files: you just tell the code what you want to calculate by launching Yambo along with one or more '''lowercase''' options.		Yambo generates its own input files: you just tell the code what you want to calculate by launching Yambo along with one or more '''lowercase''' options.
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	-l :GoWo Quasiparticle lifetimes		-l :GoWo Quasiparticle lifetimes
	-a :ACFDT Total Energy		-a :ACFDT Total Energy
	~~Note that multiple options can be used together (in some cases this is actually a necessity). For instance:~~
	~~$ yambo -o c -k hartree Calculate optical spectra including local field effects (Hartree approximation)~~
	~~$ yambo -x -g n -p p Perform a Hartree-Fock and GW calculation using a plasmon-pole approximation~~

	~~After launching~~ Yambo with a lowercase option, Yambo will generate an appropriate input file (default name: ~~<code>~~yambo.in~~</code>~~) and launch the <code>vi</code> editor. (Editor choice can be changed at configure; alternatively you can use the <code>-Q</code> run time option).		Any time you launch Yambo with a lowercase option, Yambo will generate the appropriate input file (default name: ''yambo.in'') and launch the <code>vi</code> editor.

			Editor choice can be changed at configure; alternatively you can use the <code>-Q</code> run time option to skip the automatic editing (do this if you are not familiar with <code>vi</code>!):
			$ yambo -x -Q
			yambo: input file yambo.in created
			$ emacs yambo.in ''or your favourite editing tool''

			==Combining options==
			Multiple options can be used together to activate various tasks or runlevels (in some cases this is actually a necessity).
			For instance, to generate an input file for optical spectra including local field effects (Hartree approximation), do
			$ yambo -o c -k hartree ''which switches on:''
			optics # [R OPT] Optics
			chi # [R CHI] Dyson equation for Chi.
			Chimod= "Hartree" # [X] IP/Hartree/ALDA/LRC/BSfxc
			To perform a Hartree-Fock and GW calculation using a plasmon-pole approximation, do:
			$ yambo -x -g n -p p ''which switches on:''
			HF_and_locXC # [R XX] Hartree-Fock Self-energy and Vxc
			gw0 # [R GW] GoWo Quasiparticle energy levels
			ppa # [R Xp] Plasmon Pole Approximation
			em1d # [R Xd] Dynamical Inverse Dielectric Matrix
			Each runlevel activates its own list of variables and flags.

	== ~~Choosing~~ input parameters ==		==Changing input parameters ==
	Yambo ~~will also read~~ various parameters from existing database files and/or input files and ~~use~~ them to suggest values or ranges.		Yambo reads various parameters from existing database files and/or input files and uses them to suggest values or ranges.
	Let's illustrate this by ~~calculating~~ the ~~static screening~~ for ~~bulk hBN~~.		Let's illustrate this by generating the input file for a Hartree-Fock calculation.
	~~$ cd YAMBO_TUTORIALS/hBN/YAMBO~~
	~~$ yambo ''(initialize, if you haven't already done so)''~~		$ yambo -x
	$ yambo -b		Inside the generated input file you should find:
	~~and look at~~ the generated input file~~. Inside~~ you ~~will see a suggested range of bands, which Yambo guesses from the core <code>ns.db1</code> database.~~		EXXRLvcs= 3187 RL # [XX] Exchange RL components
	% ~~BndsRnXd~~		%QPkrange # [GW] QP generalized Kpoint/Band indices
	1 \| 100 \| ~~# [Xd] Polarization function bands~~		1\| 14\| 1\|100\|
	%		%
	~~Change these values to~~ <code> ~~8 \| 9 \|~~ </code>~~, save~~ and ~~exit~~ the ~~editor~~. ~~Now launch~~ the ~~input file generator again:~~		The <code>QPkrange</code> variable (follow the link for a detailed explanation) suggests a range of k-points (1 to 14) and bands (1 to 100) based on what it finds in the core database ''SAVE/ns.db1'', i.e. as defined by the DFT code. Leave that variable alone, and instead modify the previous variable to <code>EXXRLvcs= 1000 RL</code>
	~~$ yambo -b~~
	and ~~notice that your chosen values remain: they are simply read from~~ the <code>~~yambo.in~~</code> ~~file.~~

	~~Now run~~ the ~~calculation. To keep things neat~~, ~~add~~ the ~~'''-J TEST''' option, which directs all output to~~ a ~~directory '''TEST''' - this will be explained in the next section.~~		Save the file, and now generate the input a second time with <code>yambo -x</code>. You will see:
	$ yambo -~~J TEST~~		EXXRLvcs= 1009 RL
	~~After a few seconds, the~~ code ~~finishes~~. ~~If you now look inside the SAVE folder, you~~ will see ~~several new databases~~:		This indicates that Yambo has read the new input value (1000 G-vectors), checked the database of G-vector shells ''(SAVE/ndb.gops)'',
	~~$ ls TEST~~		and changed the input value to one that fits a completely closed shell.
	'''ndb.~~dip_iR_and_P~~''~~' '''ndb.em1s''' [...]~~
	~~Delete the input file <code>yambo.in</code>,~~ and ~~generate~~ the input ~~file for~~ a ~~different task: optical response in the independent particle approximation~~.		The input file generator of Yambo is thus an ''intelligent'' parser, which interacts with the user and the existing databases. For this reason we recommend that you always use Yambo to generate the input files, rather than making them yourself.
	~~$ rm yambo.in~~
	~~$ yambo -o c -J TEST~~
	~~Looking inside the~~ input file ~~you will find:~~
	~~% BndsRnXd~~
	~~8 \| 9 \| # [Xd] Polarization function bands~~
	%
	~~Here~~, ~~Yambo has read from~~ the ~~<code>ndb.dip_iR_and_P</code> database~~ and ~~suggests to use~~ the ~~previous values~~. ~~If at~~ this ~~stage,~~ you ~~decide~~ to ~~change these values (increase~~ the ~~range)~~, ~~Yambo will ''recompute'' the relevant database~~.

	== Links ==		== Links ==
	* [[Command_line_options\|Command line options]]		* Next module: [[Command_line_options\|Command line options]]
			* Back to [[First steps: a walk through from DFT to optical properties\|First steps with yambo]] tutorial
	* [[Tutorials\|Back to tutorials menu]]		* [[Tutorials\|Back to tutorials menu]]

Conor: /* Choosing input parameters */

2017-03-28T11:14:52Z

Choosing input parameters

← Older revision		Revision as of 11:14, 28 March 2017
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	After a few seconds, the code finishes. If you now look inside the SAVE folder, you will see several new databases:		After a few seconds, the code finishes. If you now look inside the SAVE folder, you will see several new databases:
	$ ls TEST		$ ls TEST
	'''ndb.dip_iR_and_P''' '''ndb.em1s''' ~~ns.gops ns.kindx~~ [...]		'''ndb.dip_iR_and_P''' '''ndb.em1s''' [...]
	Delete the input file <code>yambo.in</code>, and generate the input file for a different task: optical response in the independent particle approximation.		Delete the input file <code>yambo.in</code>, and generate the input file for a different task: optical response in the independent particle approximation.
	$ rm yambo.in		$ rm yambo.in

Conor at 11:05, 28 March 2017

2017-03-28T11:05:10Z

← Older revision		Revision as of 11:05, 28 March 2017
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	-a :ACFDT Total Energy		-a :ACFDT Total Energy
	Note that multiple options can be used together (in some cases this is actually a necessity). For instance:		Note that multiple options can be used together (in some cases this is actually a necessity). For instance:
	yambo -o c -k hartree Calculate optical spectra including local field effects (Hartree approximation)		$ yambo -o c -k hartree Calculate optical spectra including local field effects (Hartree approximation)
	yambo -x -g n -p p Perform a Hartree-Fock and GW calculation using a plasmon-pole approximation		$ yambo -x -g n -p p Perform a Hartree-Fock and GW calculation using a plasmon-pole approximation

	After launching Yambo with a lowercase option, Yambo will generate an appropriate input file (default name: <code>yambo.in</code>) and launch the <code>vi</code> editor. (Editor choice can be changed at configure; alternatively you can use the <code>-Q</code> run time option).		After launching Yambo with a lowercase option, Yambo will generate an appropriate input file (default name: <code>yambo.in</code>) and launch the <code>vi</code> editor. (Editor choice can be changed at configure; alternatively you can use the <code>-Q</code> run time option).
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	== Choosing input parameters ==		== Choosing input parameters ==
	Yambo will also read various parameters from existing database files and/or input files and use them to suggest values or ranges.		Yambo will also read various parameters from existing database files and/or input files and use them to suggest values or ranges.
	Let's illustrate this by calculating the static screening for bulk hBN.		Let's illustrate this by calculating the static screening for bulk hBN.
	cd YAMBO_TUTORIALS/hBN/YAMBO		$ cd YAMBO_TUTORIALS/hBN/YAMBO
	yambo ''(initialize, if you haven't already done so)''		$ yambo ''(initialize, if you haven't already done so)''
	yambo -b		$ yambo -b
	and look at the generated input file. Inside you will see a suggested range of bands, which Yambo guesses from the core <code>ns.db1</code> database.		and look at the generated input file. Inside you will see a suggested range of bands, which Yambo guesses from the core <code>ns.db1</code> database.
	% BndsRnXd		% BndsRnXd
Line 50:		Line 50:
	%		%
	Change these values to <code> 8 \| 9 \| </code>, save and exit the editor. Now launch the input file generator again:		Change these values to <code> 8 \| 9 \| </code>, save and exit the editor. Now launch the input file generator again:
	yambo -b		$ yambo -b
	and notice that your chosen values remain: they are simply read from the <code>yambo.in</code> file. Now run the calculation:		and notice that your chosen values remain: they are simply read from the <code>yambo.in</code> file.
	yambo
			Now run the calculation. To keep things neat, add the '''-J TEST''' option, which directs all output to a directory '''TEST''' - this will be explained in the next section.
			$ yambo -J TEST
	After a few seconds, the code finishes. If you now look inside the SAVE folder, you will see several new databases:		After a few seconds, the code finishes. If you now look inside the SAVE folder, you will see several new databases:
	$ ls ~~SAVE~~		$ ls TEST
	~~ns.db1 ns.wf~~ '''ndb.dip_iR_and_P''' '''ndb.em1s''' ns.gops ns.kindx [...]		'''ndb.dip_iR_and_P''' '''ndb.em1s''' ns.gops ns.kindx [...]
	Delete the input file <code>yambo.in</code>, and generate the input file for a different task: optical response in the independent particle approximation.		Delete the input file <code>yambo.in</code>, and generate the input file for a different task: optical response in the independent particle approximation.
	$ rm yambo.in		$ rm yambo.in
	$ yambo -o c		$ yambo -o c -J TEST
	Looking inside the input file you will find:		Looking inside the input file you will find:
	% BndsRnXd		% BndsRnXd

Conor at 20:15, 23 March 2017

2017-03-23T20:15:50Z

← Older revision		Revision as of 20:15, 23 March 2017
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	yambo ''(initialize, if you haven't already done so)''		yambo ''(initialize, if you haven't already done so)''
	yambo -b		yambo -b
	and look at the generated input file. Inside you will see a suggested range of bands, which Yambo guesses from the core <code>ns.db1</~~core~~> database.		and look at the generated input file. Inside you will see a suggested range of bands, which Yambo guesses from the core <code>ns.db1</code> database.
	% BndsRnXd		% BndsRnXd
	1 \| 100 \| # [Xd] Polarization function bands		1 \| 100 \| # [Xd] Polarization function bands
	%		%
	Change ~~this~~ to		Change these values to <code> 8 \| 9 \| </code>, save and exit the editor. Now launch the input file generator again:
	~~% BndsRnXd~~
	8 \| 9 \| ~~# [Xd] Polarization function bands~~
	%
	and exit the editor. ~~Launch~~ the input file generator again:
	yambo -b		yambo -b
	and notice that your chosen values remain: they are simply read from the <code>yambo.in</code> file. Now ~~launch~~ the ~~code~~:		and notice that your chosen values remain: they are simply read from the <code>yambo.in</code> file. Now run the calculation:
	yambo		yambo
	After a few seconds, the code finishes. If you now look inside the SAVE folder, you will see several new databases:		After a few seconds, the code finishes. If you now look inside the SAVE folder, you will see several new databases:
	$ ls SAVE		$ ls SAVE
	ns.db1 ns.wf '''ndb.dip_iR_and_P''' '''ndb.em1s''' ns.gops ns.kindx [...]		ns.db1 ns.wf '''ndb.dip_iR_and_P''' '''ndb.em1s''' ns.gops ns.kindx [...]
	Delete the input file, and ~~launch~~ a ~~new calculation~~: optical response in the independent particle approximation.		Delete the input file <code>yambo.in</code>, and generate the input file for a different task: optical response in the independent particle approximation.
	$ rm yambo.in		$ rm yambo.in
	$ yambo -o c		$ yambo -o c
	~~and look at~~ the input file:		Looking inside the input file you will find:
	% BndsRnXd		% BndsRnXd
	8 \| 9 \| # [Xd] Polarization function bands		8 \| 9 \| # [Xd] Polarization function bands
	%		%
	Here, Yambo has read from the <code>ndb.dip_iR_and_P</code> database and suggests to use the previous values. If at this stage, you decide to change these values, Yambo will ''recompute'' the relevant database.		Here, Yambo has read from the <code>ndb.dip_iR_and_P</code> database and suggests to use the previous values. If at this stage, you decide to change these values (increase the range), Yambo will ''recompute'' the relevant database.

	== Links ==		== Links ==
	* [[Command_line_options\|Command line options]]		* [[Command_line_options\|Command line options]]
	* [[Tutorials\|Back to tutorials menu]]		* [[Tutorials\|Back to tutorials menu]]

← Older revision		Revision as of 09:48, 21 April 2017
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	* Back to [[First steps: a walk through from DFT to optical properties\|First steps with yambo]] tutorial		* Back to [[First steps: a walk through from DFT to optical properties\|First steps with yambo]] tutorial
	* [[Tutorials\|Back to tutorials menu]]		* [[Tutorials\|Back to tutorials menu]]

			<br>
			{\| style="width:100%" border="1"
			\|style="width:15%; text-align:left"\|Prev: [[Bulk_material:_h-BN\|bulk hBN]]
			\|style="width:70%; text-align:center"\|Now: [[Tutorials\|Tutorials Home]] --> [[First_steps:_a_walk_through_from_DFT_to_optical_properties\|First steps]] --> [[Bulk_material:_h-BN\|bulk hBN]] --> [[Initialization\|Initialization]]
			\|style="width:15%; text-align:right"\|Next: [[Command_line_options\|Command line options]]
			\|-
			\|}