Add graphene

README.md

@@ -11,7 +11,14 @@ Datasets of input files for Wannier functions.
 - `Si2_valence`: Silicon valence band only
 - `Si2`: Silicon valence and conduction bands
 - `Cu`: copper, metal
+- `graphene`: graphene, 2D material
+- `MoS2`: molybdenum disulfide, 2D material
+- `Fe_collinear`: iron, collinear magnetic calculation
+- `Fe_soc`: iron, spin-orbit coupling (SOC) calculation
 - `CrI3`: chromium triiodide, magnetic calculation
+- `BN`: 3D boron nitride, insulator
+- `SnSe2`: tin diselenide, 3D material
+- `CuBr2`: copper bromide, 3D material
 
 ## Why this repo?
 

datasets/graphene/UNK00001.1

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datasets/graphene/UNK00002.1

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datasets/graphene/UNK00003.1

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datasets/graphene/UNK00004.1

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datasets/graphene/UNK00005.1

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datasets/graphene/UNK00006.1

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datasets/graphene/UNK00007.1

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datasets/graphene/UNK00008.1

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datasets/graphene/UNK00009.1

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datasets/graphene/generator/README.md

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+# Example of DFTK to amn/mmn/eig/unk
+
+The amn/mmn/eig/unk files in this folder are generated by the script
+[`dftk.jl`](./dftk.jl), see headers therein.
+
+I added one `graphene_00001.xsf` which is used in the `WannierPlots.jl` tutorials.

datasets/graphene/generator/dftk.jl

@@ -0,0 +1,59 @@
+# Generate amn/mmn/eig/unk from DFTK
+# Adapted from
+# https://github.com/JuliaMolSim/DFTK.jl/blob/d3a2963b34f16491eb6aa213d59b8f0d0929f1f5/examples/wannier90.jl
+# Changes are:
+# - use `3 x 3 x 1` kgrid
+# - unk files are resampled on a much coarse grid to save space
+# - fix normalization of unk
+using DFTK
+using Unitful
+using UnitfulAtomic
+
+d = 10u"Å"
+a = 2.641u"Å"  # Graphene Lattice constant
+lattice = [
+    a -a/2 0
+    0 √3*a/2 0
+    0 0 d
+]
+
+C = ElementPsp(:C, psp = load_psp("hgh/pbe/c-q4"))
+atoms = [C, C]
+positions = [[0.0, 0.0, 0.0], [1 // 3, 2 // 3, 0.0]]
+model = model_PBE(lattice, atoms, positions)
+basis = PlaneWaveBasis(model; Ecut = 15, kgrid = [3, 3, 1])
+scfres = self_consistent_field(basis; n_bands = 15, tol = 1e-8);
+
+using wannier90_jll  # Needed to make run_wannier90 available
+run_wannier90(
+    scfres;
+    fileprefix = "wannier/graphene",
+    n_wannier = 5,
+    #num_print_cycles=25,
+    num_iter = 200,
+    ##
+    dis_win_max = 19.0,
+    dis_froz_max = 0.1,
+    dis_num_iter = 300,
+    dis_mix_ratio = 1.0,
+    ##
+    wannier_plot = true,
+    wannier_plot_format = "cube",
+    wannier_plot_supercell = 5,
+    write_xyz = true,
+    translate_home_cell = true,
+);
+
+# resample unk
+period = 3
+using Wannier
+# and make sure unk is normalized such that
+# for each w = W[:,:,:,i], i = 1:n_bands
+#     sum(conj(w) .* w) = prod(size(w))
+for f in filter(x -> startswith(x, "UNK"), readdir())
+    ik, W = read_unk(f)
+    w = W[:, :, :, 1]
+    fac = sqrt(prod(size(w)) / sum(real(conj(w) .* w)))
+    W = fac * W[1:period:end, 1:period:end, 1:period:end, :]
+    write_unk("$period.$f", ik, W)
+end

datasets/graphene/generator/qe/bands.in

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+&CONTROL
+  calculation = 'bands'
+  etot_conv_thr =   2.0000000000d-05
+  forc_conv_thr =   1.0000000000d-04
+  max_seconds =   4.1040000000d+04
+  outdir = './out/'
+  prefix = 'gra'
+  pseudo_dir = '../../../pseudo/'
+  restart_mode = 'from_scratch'
+  tprnfor = .true.
+  tstress = .true.
+  verbosity = 'high'
+/
+&SYSTEM
+  degauss =   1.0000000000d-02
+  ecutrho =   360.0
+  ecutwfc =   45.0
+  ibrav = 0
+  nat = 2
+  nbnd = 20
+  noinv = .true.
+  nosym = .true.
+  ntyp = 1
+  occupations = 'smearing'
+  smearing = 'cold'
+/
+&ELECTRONS
+  conv_thr =   4.0000000000d-10
+  diago_full_acc = .true.
+  electron_maxstep = 80
+  mixing_beta =   4.0000000000d-01
+  startingpot = 'file'
+/
+ATOMIC_SPECIES
+C     12 C.pbesol-n-kjpaw_psl.1.0.0.UPF
+ATOMIC_POSITIONS crystal
+C         0.0000000000    0.0000000000    0.0
+C         0.3333333333    0.6666666667    0.0
+CELL_PARAMETERS angstrom
+    2.1304215583   -1.2299994602    0.0000000000
+    0.0000000000    2.4599989204    0.0000000000
+    0.0000000000    0.0000000000   10.0000000000
+K_POINTS crystal
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+    0.162319   -0.081159    0.000000   1.0
+    0.156522   -0.078261    0.000000   1.0
+    0.150725   -0.075362    0.000000   1.0
+    0.144928   -0.072464    0.000000   1.0
+    0.139130   -0.069565    0.000000   1.0
+    0.133333   -0.066667    0.000000   1.0
+    0.127536   -0.063768    0.000000   1.0
+    0.121739   -0.060870    0.000000   1.0
+    0.115942   -0.057971    0.000000   1.0
+    0.110145   -0.055072    0.000000   1.0
+    0.104348   -0.052174    0.000000   1.0
+    0.098551   -0.049275    0.000000   1.0
+    0.092754   -0.046377    0.000000   1.0
+    0.086957   -0.043478    0.000000   1.0
+    0.081159   -0.040580    0.000000   1.0
+    0.075362   -0.037681    0.000000   1.0
+    0.069565   -0.034783    0.000000   1.0
+    0.063768   -0.031884    0.000000   1.0
+    0.057971   -0.028986    0.000000   1.0
+    0.052174   -0.026087    0.000000   1.0
+    0.046377   -0.023188    0.000000   1.0
+    0.040580   -0.020290    0.000000   1.0
+    0.034783   -0.017391    0.000000   1.0
+    0.028986   -0.014493    0.000000   1.0
+    0.023188   -0.011594    0.000000   1.0
+    0.017391   -0.008696    0.000000   1.0
+    0.011594   -0.005797    0.000000   1.0
+    0.005797   -0.002899    0.000000   1.0
+    0.000000    0.000000    0.000000   1.0

datasets/graphene/generator/qe/graphene.win

@@ -0,0 +1,56 @@
+num_bands         =   15
+num_wann          =   5
+
+dis_froz_max      =  2
+dis_num_iter      =  1000
+num_iter          =  1000
+conv_tol =   1.0000000000d-8
+conv_window = 3
+
+fermi_energy = -0.4602
+
+guiding_centres = true
+
+bands_plot = true
+
+begin kpoint_path
+G 0.0000000000     0.0000000000     0.0000000000  M 0.5000000000    -0.5000000000     0.0000000000
+M 0.5000000000    -0.5000000000     0.0000000000  K 0.6666666667    -0.3333333333     0.0000000000
+K 0.6666666667    -0.3333333333     0.0000000000  G 0.0000000000     0.0000000000     0.0000000000
+end kpoint_path
+
+wannier_plot = true
+wannier_plot_supercell = 3
+wvfn_formatted = true
+
+begin atoms_frac
+C    0.0000000000    0.0000000000    0.0
+C    0.3333333333    0.6666666667    0.0
+end atoms_frac
+
+begin projections
+C:pz
+f=0.16666667,0.33333333,0.0:s
+f=0.66666667,0.83333333,0.0:s
+f=0.16666667,0.83333333,0.0:s
+end projections
+
+begin unit_cell_cart
+  2.1304215583   -1.2299994602    0.0000000000
+  0.0000000000    2.4599989204    0.0000000000
+  0.0000000000    0.0000000000   10.0000000000
+end unit_cell_cart
+
+mp_grid      = 3 3 1
+
+begin kpoints
+  0.00000000  0.00000000  0.00000000  1.111111e-01
+  0.00000000  0.33333333  0.00000000  1.111111e-01
+  0.00000000  0.66666667  0.00000000  1.111111e-01
+  0.33333333  0.00000000  0.00000000  1.111111e-01
+  0.33333333  0.33333333  0.00000000  1.111111e-01
+  0.33333333  0.66666667  0.00000000  1.111111e-01
+  0.66666667  0.00000000  0.00000000  1.111111e-01
+  0.66666667  0.33333333  0.00000000  1.111111e-01
+  0.66666667  0.66666667  0.00000000  1.111111e-01
+end kpoints

datasets/graphene/generator/qe/nscf.in

@@ -0,0 +1,53 @@
+&CONTROL
+  calculation = 'nscf'
+  etot_conv_thr =   2.0000000000d-05
+  forc_conv_thr =   1.0000000000d-04
+  max_seconds =   4.1040000000d+04
+  outdir = './out/'
+  prefix = 'gra'
+  pseudo_dir = '../../../pseudo/'
+  restart_mode = 'from_scratch'
+  tprnfor = .true.
+  tstress = .true.
+  verbosity = 'high'
+/
+&SYSTEM
+  degauss =   1.0000000000d-02
+  ecutrho =   360.0
+  ecutwfc =   45.0
+  ibrav = 0
+  nat = 2
+  nbnd = 15
+  noinv = .true.
+  nosym = .true.
+  ntyp = 1
+  occupations = 'smearing'
+  smearing = 'cold'
+/
+&ELECTRONS
+  conv_thr =   4.0000000000d-10
+  diago_full_acc = .true.
+  electron_maxstep = 80
+  mixing_beta =   4.0000000000d-01
+  startingpot = 'file'
+/
+ATOMIC_SPECIES
+C     12 C.pbesol-n-kjpaw_psl.1.0.0.UPF
+ATOMIC_POSITIONS crystal
+C         0.0000000000    0.0000000000    0.0
+C         0.3333333333    0.6666666667    0.0
+CELL_PARAMETERS angstrom
+    2.1304215583   -1.2299994602    0.0000000000
+    0.0000000000    2.4599989204    0.0000000000
+    0.0000000000    0.0000000000   10.0000000000
+K_POINTS crystal
+9
+  0.00000000  0.00000000  0.00000000  1.111111e-01
+  0.00000000  0.33333333  0.00000000  1.111111e-01
+  0.00000000  0.66666667  0.00000000  1.111111e-01
+  0.33333333  0.00000000  0.00000000  1.111111e-01
+  0.33333333  0.33333333  0.00000000  1.111111e-01
+  0.33333333  0.66666667  0.00000000  1.111111e-01
+  0.66666667  0.00000000  0.00000000  1.111111e-01
+  0.66666667  0.33333333  0.00000000  1.111111e-01
+  0.66666667  0.66666667  0.00000000  1.111111e-01

datasets/graphene/generator/qe/p2w.in

@@ -0,0 +1,9 @@
+&INPUTPP
+  outdir = './out/'
+  prefix = 'gra'
+  seedname = 'graphene'
+  spn_formatted = .true.
+  write_unk = .true.
+  wvfn_formatted = .true.
+! reduce_unk = .true.
+/

datasets/graphene/generator/qe/proj.in

@@ -0,0 +1,7 @@
+&PROJWFC
+  deltae =   2.0000000000d-01
+! lsym = .true.
+  outdir = './out'
+  prefix = 'gra'
+  filproj = 'graphene'
+/

datasets/graphene/generator/qe/run.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+set -e
+
+NP=8
+NK=8
+
+PWX=pw.x
+W90X=wannier90.x
+P2WX=pw2wannier90.x
+
+F='scf'
+mpirun -n $NP $PWX -nk $NK -in $F.in > $F.out
+
+F='bands'
+mpirun -n $NP $PWX -nk $NK -in $F.in > $F.out
+
+F='proj'
+mpirun -n $NP projwfc.x -nk $NK -in $F.in > $F.out
+
+F='nscf'
+mpirun -n $NP $PWX -nk $NK -in $F.in > $F.out
+
+F='graphene.win'
+mpirun -n $NP $W90X -pp $F
+
+F='p2w'
+mpirun -n $NP $P2WX -in $F.in > $F.out
+
+F='graphene.win'
+mpirun -n $NP $W90X $F

datasets/graphene/generator/qe/scf.in

@@ -0,0 +1,39 @@
+&CONTROL
+  calculation = 'scf'
+  etot_conv_thr =   2.0000000000d-05
+  forc_conv_thr =   1.0000000000d-04
+  max_seconds =   4.1040000000d+04
+  outdir = './out/'
+  prefix = 'gra'
+  pseudo_dir = '../../../pseudo/'
+  tprnfor = .true.
+  tstress = .true.
+  verbosity = 'high'
+/
+&SYSTEM
+  degauss =   1.0000000000d-02
+  ecutrho =   360.0
+  ecutwfc =   45.0
+  ibrav = 0
+  nat = 2
+  nosym = .false.
+  ntyp = 1
+  occupations = 'smearing'
+  smearing = 'cold'
+/
+&ELECTRONS
+  conv_thr =   4.0000000000d-10
+  electron_maxstep = 80
+  mixing_beta =   4.0000000000d-01
+/
+ATOMIC_SPECIES
+C     12 C.pbesol-n-kjpaw_psl.1.0.0.UPF
+ATOMIC_POSITIONS crystal
+C         0.0000000000    0.0000000000    0.0
+C         0.3333333333    0.6666666667    0.0
+CELL_PARAMETERS angstrom
+    2.1304215583   -1.2299994602    0.0000000000
+    0.0000000000    2.4599989204    0.0000000000
+    0.0000000000    0.0000000000   10.0000000000
+K_POINTS automatic
+3 3 1 0 0 0

datasets/graphene/graphene.amn

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c3d503af5486a21ccf5867207570bfd74510b7aaabb8644518f88832e584b92c
+size 40555

datasets/graphene/graphene.eig

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7641b659905554f8e878dbce1ac5a3ba984d6b00ab57041fd13284776abf2a9f
+size 5130

datasets/graphene/graphene.mmn

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ae1137ed4eeb55b3720ebc1f43f3badc600b91cdeb85df2d85916d10b89a9eeb
+size 762555

datasets/graphene/graphene.win

@@ -0,0 +1,46 @@
+! Generated by DFTK.jl at 2022-09-02T09:45:08.815
+
+num_wann             =   5
+num_bands            =   15
+num_iter             =   200
+dis_win_max          =   19.0
+dis_froz_max         =   0.1
+dis_num_iter         =   300
+dis_mix_ratio        =   1.0
+wannier_plot_format  =   cube
+wannier_plot_supercell =   5
+write_xyz            =   true
+translate_home_cell  =   true
+wvfn_formatted = True
+wannier_plot   = True
+
+!!!!!!!!!!!!!!!!!!!! System
+
+
+begin unit_cell_cart
+bohr
+  4.990767   0.000000   0.000000
+ -2.495383   4.322131   0.000000
+  0.000000   0.000000  18.897261
+end unit_cell_cart
+
+begin atoms_frac
+C    0.000000   0.000000   0.000000
+C    0.333333   0.666667   0.000000
+end atoms_frac
+
+!!!!!!!!!!!!!!!!!!!! k_points
+
+mp_grid : 3 3 1
+
+begin kpoints
+0.00000000 0.00000000 0.00000000
+0.33333333 0.00000000 0.00000000
+0.33333333 0.33333333 0.00000000
+-0.33333333 0.00000000 0.00000000
+-0.33333333 -0.33333333 0.00000000
+0.33333333 -0.33333333 0.00000000
+-0.33333333 0.33333333 0.00000000
+0.00000000 -0.33333333 0.00000000
+0.00000000 0.33333333 0.00000000
+end kpoints

datasets/graphene/reference/graphene.dis.amn

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8c0387341070588e2c8d9ad6624383865b535e5c3525aa216872545022bca7d9
+size 35160

datasets/graphene/reference/graphene.nnkp

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0bf877c980898ae358dd2a30aa0814bb3156689c88e7c3a91e49d5870f0a6929
+size 2911

datasets/graphene/reference/graphene_00001.xsf

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a6c717b6e68de4c9fa12a37f7b59beb249d8d2f7543205806262397c8c77b88a
+size 546781