Initialization - Revision history

Yambowikiadmin: /* Report file */

2024-10-16T07:55:46Z

Report file

← Older revision		Revision as of 07:55, 16 October 2024
Line 74:		Line 74:
	This mostly reports information about the ground state system as defined by the DFT run, but also adds information about the band gaps, occupations, shells of G-vectors, IBZ/BZ grids, the CPU structure (for parallel runs), and so on. Some points of note:		This mostly reports information about the ground state system as defined by the DFT run, but also adds information about the band gaps, occupations, shells of G-vectors, IBZ/BZ grids, the CPU structure (for parallel runs), and so on. Some points of note:

			[02.03] Reciprocal space
			========================

	~~Up to Yambo version 4.5~~		Full and reduced cutoff: 41477.1 79818.4 [mHa]
	~~[02.03] RL shells~~
	~~=================~~
	~~Shells, format: [S#] G_RL(mHa)~~
	~~[S453]:8029(0~~.~~7982E+5) [S452]:8005(0~~.~~7982E+5) [S451]:7981(0.7982E+5) [S450]:7957(0.7942E+5)~~
	~~...~~
	[~~S4]:11( 1183.) [S3]:5( 532.5123) [S2]:3( 133.1281) [S1~~]~~:1( 0.000000)~~

	~~From Yambo version 5.0~~		nG shells : 204
	~~[02.03] Reciprocal space~~		nG charge : 2987
	~~========================~~

	nG shells : ~~217~~
	nG charge : ~~3187~~
	nG WFs : 1477		nG WFs : 1477
	nC WFs : 1016		nC WFs : 1016
	G-vecs. in first 21 shells: [ Number ]		G-vecs. in first 204 shells: [ Number ]
	1 3 5 11 13 25 37 39 51		1 3 5 11 13 25 37 39 51
	63 65 71 83 95 107 113 125 127		63 65 71 83 95 107 113 125 127
	139 151 163		139 151 163 175 187 189 201 213 225
	~~...~~		237 249 261 285 287 311 335 347 359
	~~Shell energy in first 21 shells: [ mHa ]~~		371 395 401 403 415 427 439 463 475
	~~0.00000 133.128 532.512 1183.37 1198.15 1316.50 1715.88 2130.05 2381.52~~
	~~3313.42 3328.20 3550.11 3683.24 4082.62 4511.57 4733.48 4748.27 4792.61~~
	~~4866.61 5266.00 5680.16~~
	~~...~~


	This reports the set of closed reciprocal lattice (RL) shells defined internally that contain G-vectors with the same modulus.		This reports the set of closed reciprocal lattice (RL) shells defined internally that contain G-vectors with the same modulus.
	~~The highest number of RL vectors we can use is 8029.~~ Yambo will always redefine any input variable in RL units to the nearest closed shell.		Yambo will always redefine any input variable in RL units to the nearest closed shell.

	~~Up to Yambo version 4.5~~
	~~[02.05] Energies [ev] & Occupations~~
	~~===================================~~
	~~Fermi Level [ev]: 5.112805~~
	~~VBM / CBm [ev]: 0.000000 3.876293~~
	~~Electronic Temp. [ev K]: 0.00 0.00~~
	~~Bosonic Temp. [ev K]: 0.00 0.00~~
	~~El. density [cm-3]: 0.460E+24~~
	~~States summary : Full Metallic Empty~~
	~~0001-0008 0009-0100~~
	~~Indirect Gaps [ev]: 3.876293 7.278081~~
	~~Direct Gaps [ev]: 4.28829 11.35409~~
	~~X BZ K-points : 72~~

	~~From Yambo version 5.0~~
	[02.05] Energies & Occupations		[02.05] Energies & Occupations
	==============================		==============================

	[X] === General ===		[X] === General ===
	[X] Electronic Temperature : 0.000000 0.000000 [eV K]		[X] Electronic Temperature : 0.000000 0.000000 [eV K]
Line 129:		Line 102:
	[X] Finite Temperature mode : no		[X] Finite Temperature mode : no
	[X] El. density : 0.46037E+24 [cm-3]		[X] El. density : 0.46037E+24 [cm-3]
	[X] Fermi Level : 5.~~110835~~ [eV]		[X] Fermi Level : 5.111115 [eV]

	[X] === Gaps and Widths ===		[X] === Gaps and Widths ===
	[X] Conduction Band Min : 3.~~877976~~ [eV]		[X] Conduction Band Min : 3.877635 [eV]
	[X] Valence Band Max : 0.000000 [eV]		[X] Valence Band Max : 0.000000 [eV]
	[X] Filled Bands : 8		[X] Filled Bands : 8
	[X] Empty Bands : 9 100		[X] Empty Bands : 9 100
	[X] Direct Gap : 4.~~289853~~ [eV]		[X] Direct Gap : 4.289509 [eV]
	[X] Direct Gap localized at k~~-point~~ : 7		[X] Direct Gap localized at k : 7
	[X] Indirect Gap : 3.~~877976~~ [eV]		[X] Indirect Gap : 3.877635 [eV]
	[X] Indirect Gap between ~~k-points~~ : 14 7		[X] Indirect Gap between kpts : 14 7
	[X] Last valence band width : 3.~~401086~~ [eV]		[X] Last valence band width : 3.401222 [eV]
	[X] 1st conduction band width : 4.~~266292~~ [eV]		[X] 1st conduction band width : 4.266500 [eV]

Yambowikiadmin: /* Different ways of running yambo */

2023-02-09T08:53:39Z

Different ways of running yambo

← Older revision		Revision as of 08:53, 9 February 2023
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	Let's try to re-run the setup with the command		Let's try to re-run the setup with the command
	$ ~~nohup~~ yambo &		$ yambo >& /dev/null &
	$ ls		$ ls
	l_setup ~~nohup.out~~ r_setup r_setup_01 SAVE		l_setup r_setup r_setup_01 SAVE

	If Yambo is launched using a script, or as a background process, or in parallel, this output will appear in a log file prefixed by the letter ''l'', in this case as ''l_setup''.		If Yambo is launched using a script, or as a background process, or in parallel, this output will appear in a log file prefixed by the letter ''l'', in this case as ''l_setup''.
Line 171:		Line 171:
	l_setup_CPU_1 l_setup_CPU_2 l_setup_CPU_3 l_setup_CPU_4		l_setup_CPU_1 l_setup_CPU_2 l_setup_CPU_3 l_setup_CPU_4
	This behaviour can be controlled at runtime - see the Parallel tutorial for details.		This behaviour can be controlled at runtime - see the Parallel tutorial for details.





	==2D hBN==		==2D hBN==

Davide: /* Summary */

2021-03-30T08:35:21Z

Summary

← Older revision		Revision as of 08:35, 30 March 2021
Line 190:		Line 190:
	* How to initialize the Yambo databases		* How to initialize the Yambo databases
	* The Yambo logs and output file structure		* The Yambo logs and output file structure


	<br>		<br>
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	\|style="width:15%; text-align:left"\|Prev: [[2D_material:_h-BN_sheet\|2D hBN]]		\|style="width:15%; text-align:left"\|Prev: [[2D_material:_h-BN_sheet\|2D hBN]]
	\|style="width:70%; text-align:center"\|Now: [[Tutorials\|Tutorials Home]] --> [[First_steps:_a_walk_through_from_DFT_to_optical_properties\|First steps]] --> [[2D_material:_h-BN_sheet\|2D 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]] --> [[2D_material:_h-BN_sheet\|2D hBN]] --> [[Initialization\|Initialization]]
	\|style="width:15%; text-align:right"\|Next: [[~~Input_file_generation_and_command_line_options~~\|Input file generation and command line options]]		\|style="width:15%; text-align:right"\|Next: [[Input_file_generation_and_command_line_options_5.0\|Input file generation and command line options (5.0)]]
	\|-		\|-
	\|}		\|}

Davide: /* Run-time output */

2021-03-29T21:49:21Z

Run-time output

← Older revision		Revision as of 21:49, 29 March 2021
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	===Run-time output===		===Run-time output===
	This is typically written to standard output (on screen) and tracks the progress of the run in real time:		This is typically written to standard output (on screen) and tracks the progress of the run in real time:
	<---> [01] ~~CPU~~ structure, Files & I/O Directories		<---> [01] MPI/OPENMP structure, Files & I/O Directories
	<---> [02] CORE Variables Setup		<---> [02] CORE Variables Setup
	<---> [02.01] Unit cells		<---> [02.01] Unit cells
	<---> [02.02] Symmetries		<---> [02.02] Symmetries
	<---> [02.03] ~~RL shells~~		<---> [02.03] Reciprocal space
	<---> Shells finder \|########################################\| [100%] --(E) --(X)		<---> Shells finder \|########################################\| [100%] --(E) --(X)
	<---> [02.04] K-grid lattice		<---> [02.04] K-grid lattice
	<---> [02.05] Energies ~~[ev]~~ & Occupations		<---> Grid dimensions : 6 6 2
	<---> [03] Transferred momenta grid		<---> [02.05] Energies & Occupations
			<---> [03] Transferred momenta grid and indexing
	<---> BZ -> IBZ reduction \|########################################\| [100%] --(E) --(X)		<---> BZ -> IBZ reduction \|########################################\| [100%] --(E) --(X)
	<---> X indexes \|########################################\| [100%] --(E) --(X)		<---> [03.01] X indexes
	<---> SE indexes \|########################################\| [100%] --(E) --(X)		<---> X [eval] \|########################################\| [100%] --(E) --(X)
	<---> [04] ~~External corrections~~		<---> X[REDUX] \|########################################\| [100%] --(E) --(X)
	<---> [05] Game Over & Game summary		<---> [03.01.01] Sigma indexes
			<---> Sigma [eval] \|########################################\| [100%] --(E) --(X)
			<---> Sigma[REDUX] \|########################################\| [100%] --(E) --(X)
			<---> [04] Timing Overview
			<---> [05] Memory Overview
			<---> [06] Game Over & Game summary
	Specific runlevels are indicated with numeric labels like [02.02]. <br>		Specific runlevels are indicated with numeric labels like [02.02]. <br>
	The hashes (#) indicate progress of the run in Wall Clock time, indicating the elapsed (E) and expected (X) time to complete a runlevel, and the percentage of the task complete.		The hashes (#) indicate progress of the run in Wall Clock time, indicating the elapsed (E) and expected (X) time to complete a runlevel, and the percentage of the task complete.

Davide at 16:36, 29 March 2021

2021-03-29T16:36:21Z

← Older revision		Revision as of 16:36, 29 March 2021
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	~~<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: [[Input_file_generation_and_command_line_options\|Input file generation and command line options]]~~
	\|-
	\|}

	==2D hBN==		==2D hBN==
	Simply repeat the steps above. Go to the folder ''containing'' the hBN-~~sheet~~ ''SAVE'' directory and launch <code>yambo</code>:		Simply repeat the steps above. Go to the folder ''containing'' the hBN-2D ''SAVE'' directory and launch <code>yambo</code>:
	$ cd TUTORIALS/hBN-2D/YAMBO		$ cd TUTORIALS/hBN-2D/YAMBO
	$ ls		$ ls
Line 186:		Line 179:

	You are now ready to use Yambo!		You are now ready to use Yambo!

			==Summary==
			From this tutorial you've learned:
			* How to initialize the Yambo databases
			* The Yambo logs and output file structure


	<br>		<br>
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	~~==Summary==~~
	~~From this tutorial you've learned:~~
	* How to initialize the Yambo databases
	* The Yambo logs and output file structure

	[[Category:Modules]]		[[Category:Modules]]

Davide: /* Report file */

2021-03-29T16:33:10Z

Report file

@@ Line 68: / Line 68: @@
 This mostly reports information about the ground state system as defined by the DFT run, but also adds information about the band gaps, occupations, shells of G-vectors, IBZ/BZ grids, the CPU structure (for parallel runs), and so on. Some points of note:
    [02.03] RL shells
    =================
@@ Line 74: / Line 76: @@
     ...
     [S4]:11( 1183.) [S3]:5( 532.5123) [S2]:3( 133.1281) [S1]:1( 0.000000)
 This reports the set of closed reciprocal lattice (RL) shells defined internally that contain G-vectors with the same modulus.
 The highest number of RL vectors we can use is 8029.  Yambo will always redefine any input variable in RL units to the nearest closed shell.
    [02.05] Energies [ev] & Occupations
    ===================================
@@ Line 90: / Line 113: @@
    Direct Gaps        [ev]:  4.28829  11.35409
    X BZ K-points :  72
 Yambo recalculates again the Fermi level (close to the value of 5.06 noted in the PWscf SCF calculation). From here on, however, the Fermi level is set to zero, and other eigenvalues are shifted accordingly. The system is insulating (8 filled, 92 empty) with an indirect band gap of 3.87 eV. The minimum and maximum direct and indirect gaps are indicated. There are 72 k-points in the full BZ, generated using symmetry from the 14 k-points in our user-defined grid.

Davide: /* Initialization */

2021-03-29T16:29:11Z

Initialization

@@ Line 10: / Line 10: @@
 == Initialization ==
 Every Yambo run '''must''' start with this step. Go to the folder ''containing'' the hBN-bulk <code>SAVE</code> directory:
@@ Line 15: / Line 16: @@
   $ ls
   SAVE
-'''TIP''': do not run yambo from ''inside'' the <code>SAVE</code> folder! In fact, if you ever see the message:
+'''TIP''': do not run yambo from ''inside'' the <code>SAVE</code> folder!
   yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)
 it usually means you are trying to launch Yambo '''from the wrong place'''.
 ===Run-time output===
 This is typically written to standard output (on screen) and tracks the progress of the run in real time:
@@ Line 42: / Line 51: @@
 Specific runlevels are indicated with numeric labels like [02.02]. <br>
 The hashes (#) indicate progress of the run in Wall Clock time, indicating the elapsed (E) and expected (X) time to complete a runlevel, and the percentage of the task complete.
 ===New core databases===
@@ Line 95: / Line 94: @@
 '''TIP''': You should inspect the report file after ''every'' run for errors and warnings.
 <br>

Davide: /* Report file */

2020-01-15T16:33:01Z

Report file

← Older revision		Revision as of 16:33, 15 January 2020
Line 77:		Line 77:

	This reports the set of closed reciprocal lattice (RL) shells defined internally that contain G-vectors with the same modulus.		This reports the set of closed reciprocal lattice (RL) shells defined internally that contain G-vectors with the same modulus.
	The highest number of RL vectors we can use is ~~3187~~. Yambo will always redefine any input variable in RL units to the nearest closed shell.		The highest number of RL vectors we can use is 8029. Yambo will always redefine any input variable in RL units to the nearest closed shell.

	[02.05] Energies [ev] & Occupations		[02.05] Energies [ev] & Occupations

Davide: /* Report file */

2020-01-15T16:32:33Z

Report file

← Older revision		Revision as of 16:32, 15 January 2020
Line 72:		Line 72:
	=================		=================
	Shells, format: [S#] G_RL(mHa)		Shells, format: [S#] G_RL(mHa)
	[~~S217~~]:~~3187~~(0.~~4380E~~+5) [~~S216~~]:~~3175~~(0.~~4378E~~+5) [~~S215~~]:~~3163~~(0.~~4321E~~+5) [~~S214~~]:~~3139~~(0.~~4321E~~+5)		[S453]:8029(0.7982E+5) [S452]:8005(0.7982E+5) [S451]:7981(0.7982E+5) [S450]:7957(0.7942E+5)
	...		...
	[S4]:11( 1183.) [S3]:5( 532.5123) [S2]:3( 133.1281) [S1]:1( 0.000000)		[S4]:11( 1183.) [S3]:5( 532.5123) [S2]:3( 133.1281) [S1]:1( 0.000000)

	This reports the set of closed reciprocal lattice (RL) shells defined internally that contain G-vectors with the same modulus.		This reports the set of closed reciprocal lattice (RL) shells defined internally that contain G-vectors with the same modulus.
Line 103:		Line 103:
	\|-		\|-
	\|}		\|}


	==2D hBN==		==2D hBN==

Marini at 13:17, 5 November 2019

2019-11-05T13:17:12Z

← Older revision		Revision as of 13:17, 5 November 2019
Line 12:		Line 12:

	Every Yambo run '''must''' start with this step. Go to the folder ''containing'' the hBN-bulk <code>SAVE</code> directory:		Every Yambo run '''must''' start with this step. Go to the folder ''containing'' the hBN-bulk <code>SAVE</code> directory:
	$ cd ~~TUTORIALS~~/hBN/YAMBO		$ cd YAMBO_TUTORIALS/hBN/YAMBO
	$ ls		$ ls
	SAVE		SAVE