2D material: h-BN sheet: Difference between revisions

Latest revision as of 13:38, 31 October 2019

In this tutorial you will learn how to generate the Yambo SAVE folder for a 2D hBN sheet starting from a PWscf calculation.

Prerequisites

Previous modules

You must first follow the tutorial on bulk hBN.

You will need:

pw.x executable, version 5.0 or later
p2y executable
Follow the instructions in the File page and download and unpack the hBN-2D.tar.gz.

System characteristics

Atomic structure of 2D hBN

Hexagonal boron nitride sheet - 2D hBN:

2D HCP lattice
Two atoms per cell, B and N (8 electrons)
Lattice constants: a = 4.716 [a.u.], c/a = 7 (supercell size)
Plane wave cutoff 40 Ry (~5000 RL vectors in wavefunctions)
SCF run: shifted 6x6x1 grid (12 k-points) with 4 bands
Non-SCF run: gamma-centred 6x6x1 (7 k-points) grid with 60 bands

DFT calculations

Unpack the tarfile. It uses the same file structure as other yambo tutorials:

$ cd YAMBO_TUTORIALS/hBN-2D/PWSCF
$ ls
Inputs		Pseudos		PostProcessing		References
hBN_2D_scf.in	hBN_2D_nscf.in     hBN_2D_scf_bands.in  hBN_2D_nscf_bands.in

The procedure is exactly the same as following in the Bulk_material:_h-BN tutorial, so no detailed explanations will be given here.

pw.x < hBN_2D_scf.in > hBN_2D_scf.out
pw.x < hBN_2D nscf.in > hBN_2D_nscf.out

The valence band maximum is computed at -4.29 eV. After these two runs, you should have a hBN_2D.save directory.

$ ls hBN_2D.save
data-file.xml charge-density.dat gvectors.dat B.pz-vbc.UPF N.pz-vbc.UPF
K00001	K00002 .... 	K00011	K00012

Conversion to Yambo format

Run the converter and check that the databases contain the information you expect:

$ cd hBN_2D.save
$ p2y
<---> DBs path set to .
<---> Index file set to data-file.xml
...
<--->  == P2Y completed ==

$ yambo -D
[RD./SAVE//ns.db1]------------------------------------------
Bands                           :  60
K-points                        :  7
G-vectors             [RL space]: 21817
Components       [wavefunctions]: 2736
...
[RD./SAVE//ns.wf]-------------------------------------------
Fragmentation                    :yes
Bands in each block             :  60
...
[RD./SAVE//ns.kb_pp_pwscf]----------------------------------
Fragmentation                    :yes
- S/N 0000908 -------------------------- v.04.01.02 r.00000 -

Note that the number of wavefunction components (G-vectors) is much higher than in the bulk hBN case (why?)

Continue using a SAVE we prepared previously:

$ cd ../../YAMBO
$ ls
SAVE

Summary

From this tutorial you've learned:

How to run a DFT calculation with PWscf in preparation for Yambo
Convert the DFT output into the Yambo format
How to check the contents of the netCDF databases

More

Advanced usage of p2y

Prev: Tutorials Home

Now: Tutorials Home --> First steps --> 2D hBN

Next: Initialization#2D_hBN

@@ Line 1: / Line 1: @@
-[[File:HBN2.png|thumb|Atomic structure of 2D hBN]]
+In this tutorial you will learn how to generate the Yambo SAVE folder for a 2D hBN sheet starting from a PWscf calculation.
-In this tutorial you will learn how to generate the Yambo SAVE folder for bulk hBN starting from a PWscf calculation.
 == Prerequisites ==
+'''Previous modules'''
+* You must first follow the tutorial on [[Bulk_material:_h-BN|bulk hBN]].
 '''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
+* Follow the instructions in the [[Tutorials#Files|File page]] and download and unpack the hBN-2D.tar.gz.
+'''
 == System characteristics ==
-[[File:HBN-bulk-3x3-annotated.png|thumb|Atomic structure of bulk hBN]]
+[[File:HBN2.png|thumb|Atomic structure of 2D hBN]]
-'''Hexagonal boron nitride - hBN''':
+'''Hexagonal boron nitride sheet - 2D hBN''':
-* HCP lattice, ABAB stacking
+* 2D HCP lattice
-* Four atoms per cell, B and N (16 electrons)
+* Two atoms per cell, B and N (8 electrons)
-* Lattice constants: ''a'' = 4.716 [a.u.], ''c/a'' = 2.582
+* Lattice constants: ''a'' = 4.716 [a.u.], ''c/a'' = 7 (supercell size)
-* Plane wave cutoff 40 Ry (1500 RL vectors in wavefunctions)
+* Plane wave cutoff 40 Ry (~5000 RL vectors in wavefunctions)
-* SCF run: shifted ''6x6x6'' grid with 8 bands
+* SCF run: shifted ''6x6x1'' grid (12 k-points) with 4 bands
-* Non-SCF run: unshifted ''6x6x2'' grid with 100 bands
+* Non-SCF run: gamma-centred ''6x6x1'' (7 k-points) grid with 60 bands
 == DFT calculations ==
 Unpack the tarfile. It uses the same file structure as other yambo tutorials:
- $ tar -xcvf hBN-bulk.tar
+  $ cd YAMBO_TUTORIALS/hBN-2D/PWSCF
-  $ cd YAMBO_TUTORIALS/hBN/PWSCF
   $ ls
   Inputs		Pseudos		PostProcessing		References
-  hBN_scf.in	hBN_nscf.in     hBN_scf_plot_bands.in  hBN_nscf_plot_bands.in
+  hBN_2D_scf.in	hBN_2D_nscf.in     hBN_2D_scf_bands.in  hBN_2D_nscf_bands.in
-First run the SCF calculation to generate the ground-state charge density, occupations, Fermi level, and so on:
+The procedure is exactly the same as following in the [[Bulk_material:_h-BN]] tutorial, so no detailed explanations will be given here.
- pw.x < hBN_scf.in > hBN_scf.out
-The output reports 36 k-points. The valence band maximum is at 5.13eV.
-Next run a non-SCF calculation to generate a set of Kohn-Sham eigenvalues and eigenvectors across a denser k-point mesh, for occupied and unoccupied states:
+  pw.x < hBN_2D_scf.in > hBN_2D_scf.out
-  pw.x < hBN_nscf.in > hBN_nscf.out
+  pw.x < hBN_2D nscf.in > hBN_2D_nscf.out
-Note the presence of the following flags in the input file:
-  wf_collect=.true.
- force_symmorphic=.true.
-which are needed for generating the Yambo databases. 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:
+The valence band maximum is computed at -4.29 eV. After these two runs, you should have a <code>hBN_2D.save</code> directory.
-  $ ls hBN.save
+  $ ls hBN_2D.save
   data-file.xml charge-density.dat gvectors.dat B.pz-vbc.UPF N.pz-vbc.UPF
-  K00001	K00002 .... 	K00035	K00036
+  K00001	K00002 .... 	K00011	K00012
 == Conversion to Yambo format ==
-The PWscf <code>bBN.save</code> output is converted to the Yambo format using the <code>p2y</code> executable (pwscf to yambo), found in the yambo <code>bin</code> directory.
+Run the converter and check that the databases contain the information you expect:
-Enter <code>hBN.save</code> and launch <code>p2y</code>:
+  $ cd hBN_2D.save
-  $ cd hBN.save
   $ p2y
- ...
   <---> DBs path set to .
   <---> Index file set to data-file.xml
- <---> Header/K-points/Energies... done
   ...
- <---> == DB1 (Gvecs and more) ...
- <---> ... Database done
- <---> == DB2 (wavefunctions)  ... done ==
- <---> == DB3 (PseudoPotential) ... done ==
   <--->  == P2Y completed ==
-This output repeats some information about the system and generates a <code>SAVE</code> directory:
-  $ ls SAVE
- ns.db1  ns.wf  ns.kb_pp_pwscf
- ns.wf_fragments_1_1 ...
- ns.kb_pp_pwscf_fragment_1 ...
-These files, with an ''n'' prefix, indicate that they are in netCDF format, and thus not human readable. However, they are perfectly transferable across different architectures.
-You are now ready to run Yambo. Check that the databases contain the information you expect:
   $ yambo -D
   [RD./SAVE//ns.db1]------------------------------------------
-  Bands                           : 100
+  Bands                           :  60
-  K-points                        : 14
+  K-points                        :  7
-  G-vectors             [RL space]:  8029
+  G-vectors             [RL space]: 21817
-  Components       [wavefunctions]: 1016
+  Components       [wavefunctions]: 2736
   ...
   [RD./SAVE//ns.wf]-------------------------------------------
   Fragmentation                    :yes
+ Bands in each block             :  60
   ...
   [RD./SAVE//ns.kb_pp_pwscf]----------------------------------
   Fragmentation                    :yes
-  - S/N 006626 -------------------------- v.04.01.02 r.00000 -
+  - S/N 0000908 -------------------------- v.04.01.02 r.00000 -
-In practice we suggest to move the <code>SAVE</code> into a new clean folder.
+Note that the number of wavefunction components (G-vectors) is much higher than in the bulk hBN case (why?)
-In this tutorial however, we ask instead that you continue using a <code>SAVE</code> we prepared previously:
+Continue using a <code>SAVE</code> we prepared previously:
   $ cd ../../YAMBO
   $ ls
   SAVE
-== Links ==
+==Summary==
+From this tutorial you've learned:
+* How to run a DFT calculation with PWscf in preparation for Yambo
+* Convert the DFT output into the Yambo format
+* How to check the contents of the netCDF databases
+== More ==
 * [[Advanced usage|Advanced usage of p2y]]
-* [[Tutorials|Back to tutorials menu]]
+<br>
+{| style="width:100%" border="1"
+|style="width:15%; text-align:left"|Prev: [[Tutorials|Tutorials Home]]
+|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]]
+|style="width:15%; text-align:right"|Next: [[Initialization#2D_hBN|Initialization#2D_hBN]]
+|-
+|}
+[[Category:Modules]]

2D material: h-BN sheet: Difference between revisions

Latest revision as of 13:38, 31 October 2019

Contents

Prerequisites

System characteristics

DFT calculations

Conversion to Yambo format

Summary

More

Navigation menu

2D material: h-BN sheet: Difference between revisions

Latest revision as of 13:38, 31 October 2019

Prerequisites

System characteristics

DFT calculations

Conversion to Yambo format

Summary

More

Navigation menu

Search