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

Revision as of 14:30, 23 March 2017

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 Bulk_material:_h-BN tutorial.

You will need:

PWSCF input files and pseudopotentials for 2D hBN sheet (Download here)
pw.x executable, version 5.0 or later
p2y executable

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:

$ tar -xcvf hBN-2D.tar
$ 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

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

Check that the databases contain the information you expect:

$ 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

@@ Line 1: / Line 1: @@
 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 [[Bulk_material:_h-BN]] tutorial.
 '''You will need''':
 * PWSCF input files and pseudopotentials for 2D hBN sheet ('''Download here''')
 * <code>pw.x</code> executable, version 5.0 or later
 * <code>p2y</code> executable
+'''
 == System characteristics ==
 [[File:HBN2.png|thumb|Atomic structure of 2D hBN]]
@@ Line 14: / Line 15: @@
 * 2D HCP lattice
 * 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 4 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
+  $ tar -xcvf hBN-2D.tar
-  $ cd YAMBO_TUTORIALS/hBN/PWSCF
+  $ cd YAMBO_TUTORIALS/hBN-2D/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.
-Enter <code>hBN.save</code> and launch <code>p2y</code>:
-  $ cd hBN.save
+  $ cd hBN_2D.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:
+Check that the databases contain the information you expect:
- $ 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 -
+Note that the number of wavefunction components (G-vectors) is much higher than in the bulk hBN case (why?)
-In practice we suggest to move the <code>SAVE</code> into a new clean folder.
+Continue using a <code>SAVE</code> we prepared previously:
-In this tutorial however, we ask instead that you continue using a <code>SAVE</code> we prepared previously:
   $ cd ../../YAMBO
   $ ls

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

Revision as of 14:30, 23 March 2017

Contents

Prerequisites

System characteristics

DFT calculations

Conversion to Yambo format

Links

Navigation menu

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

Revision as of 14:30, 23 March 2017

Prerequisites

System characteristics

DFT calculations

Conversion to Yambo format

Links

Navigation menu

Search