I've just started learning sisl. I wonder if it is possible to get band structure with selected fatbands. I include example of a figure I mean obtained from VASP calculations in p4v.

Thank you for help.

Elwira

I installed siesta using the command conda install -c conda-forge "siesta=*=openmpi", but running siesta without any additional options causes it to use all available CPUs on my computer. I would like to limit the parallel calculation to only 16 CPUs.

Can anyone provide guidance on how to set the number of CPUs used in siesta calculations?

I am using Ubuntu 20.04.1 and have installed openmpi-4.1.5.

Traceback (most recent call last):
File "run.py", line 3, in
import sisl
File "/home/mandar/.local/lib/python2.7/site-packages/sisl/init.py", line 93, in
from . import utils
File "/home/mandar/.local/lib/python2.7/site-packages/sisl/utils/init.py", line 41, in
from . import mathematics as math
File "/home/mandar/.local/lib/python2.7/site-packages/sisl/utils/mathematics.py", line 8, in
from sisl._indices import indices_le
ImportError: No module named _indices

I should have made the ipynb write out all files (except C.psf). Here they are for completeness sake:

• RUNk.fdf

SystemLabel k

TBT.HS DEVICE.nc

TBT.Symmetry.TimeReversal f

TBT.k [400 1 1]

TBT.Contours.Eta 1e-4 eV

TBT.DOS.Gf true
TBT.DOS.A true

%block TBT.Elec.Left
  HS ELEC.nc
  semi-inf-direction -A2
  electrode-position 1
%endblock TBT.Elec.Left
%block TBT.Elec.Right
  HS ELEC.nc
  semi-inf-direction +A2
  electrode-position end -1
%endblock TBT.Elec.Right

• RUN_TS_ELEC.fdf

SystemLabel ELEC

%include STRUCT_ELEC.fdf

%block kgrid.MonkhorstPack
    100   0  0 0.
    0  10  0 0.
    0   0  1 0.
%endblock kgrid.MonkhorstPack

PAO.BasisSize         SZP
PAO.EnergyShift       0.01 Ry
XC.functional     GGA
XC.authors        PBE
MeshCutoff        250.000000 Ry
FilterCutoff      150.000000 Ry

ElectronicTemperature   300 K
OccupationFunction      FD

MinSCFIterations       3
MaxSCFIterations       200
SCF.DM.Tolerance       0.0001
# Mixing parameters:
SCF.Mixer.Weight       0.10
SCF.Mixer.History      12
SCF.Mix.First          true
DM.UseSaveDM           .true.

MD.NumCGSteps 0

SaveHS                          T

• RUN_TS.fdf

SolutionMethod transiesta

TBT.Contour.Eta 1e-4 eV
TBT.k [1 150 1]
%block TBT.Contours
  all
%endblock

%block TBT.Contour.all
   from -16 eV to 0. eV
    delta 0.02 eV
      method mid-rule
%endblock

%block TBT.Contour.low
   from -16 eV to -14 eV
    delta 0.02 eV
      method mid-rule
%endblock

%block TBT.Contour.high
   from -2 eV to 0. eV
    delta 0.02 eV
      method mid-rule
%endblock

TBT.DOS.Gf true
TBT.DOS.A true
TBT.DOS.A.All true

%block kgrid.MonkhorstPack
    3  0  0 0.
    0 10  0 0.
    0  0  1 0.
%endblock kgrid.MonkhorstPack

TS.Voltage 0 eV

%block TS.ChemPots
  Fermi
%endblock TS.ChemPots

%block TS.ChemPot.Fermi
  mu 0. eV
  contour.eq
    begin
      C-Fermi
      T-Fermi
    end
%endblock

TS.Contours.Eq.Pole 2.5 eV
%block TS.Contour.C-Fermi
  part circle
   from -40. eV to -10 kT
     points 25
      method g-legendre
%endblock
%block TS.Contour.T-Fermi
  part tail
   from prev to inf
     points 10
      method g-fermi
%endblock

%block TS.Elecs
  Left
  Right
%endblock TS.Elecs

%block TS.Elec.Left
  HS ELEC.TSHS
  semi-inf-direction -a1
  electrode-position 1
%endblock
%block TS.Elec.Right
  HS ELEC.TSHS
  semi-inf-direction +a1
  electrode-position end -1
%endblock

PAO.BasisSize         SZP

XC.functional     GGA
XC.authors        PBE
MeshCutoff        250.000000 Ry
FilterCutoff      150.000000 Ry

ElectronicTemperature   300 K

MinSCFIterations       3
SCF.DM.Tolerance       0.0001
# Mixing parameters:
SCF.Mixer.Weight       0.10
SCF.Mixer.History      12
SCF.Mix.First          true
DM.UseSaveDM           true

SaveHS                          T

%include STRUCT_DEVICE.fdf

Hello Nick,
I met some problems running the sisl tutorials.
In TB_01:

for ia, io in H:

You intended to enumerate atomic and orbital indices, but actually when using for i in H:, it
enumerates the indices of nonzero terms in H, for example running:

graphene = sisl.geom.graphene()
H = sisl.Hamiltonian(graphene)
H[0, 0] = 0.0
H[1, 1] = 0.0
H[0, 1] = -2.7
H[1, 0] = -2.7
H[0, 1, (-1, 0)] = -2.7
H[0, 1, (0, -1)] = -2.7
H[1, 0, (1, 0)] = -2.7
H[1, 0, (0, 1)] = -2.7
for ia, io in H:
    print(ia,io)

Output is:

0 0
0 1
0 9
0 5
1 1
1 0
1 10
1 14

In TB_04 about edge atom indice:

for ia in device.close(device.center(what='cell'), R=14.):
    if len(device.close(ia, R=1.43)) < 4:
        edge.append(ia + 1) # + 1 to get fortran indices

Why do you use fortran indices in the following code? When you plot the edge atom DOS later, and call tbt.DOS(atom=edge, norm='atom'), should you use python indices here?

In TB_05,

dangling = [ia for ia in H.geom.close(H.geom.center(what='cell'), R=14.)
                if len(H.edges(ia)) < 2]
H = H.remove(dangling)
# + 1 to get fortran indices
edge = [ia + 1 for ia in H.geom.close(H.geom.center(what='cell'), R=14.)
         if len(H.edges(ia)) < 3]

Should the two inequality be <3 and <4, as in TB_04? Since H.edges(ia) returns itself too.

Thank you!

Questions for TS_02

Questions for TS_03

Questions for exercise TS_01

Object sisl.Geometry.tile not found.

NameError Traceback (most recent call last)
in
1 get_ipython().run_line_magic('pdoc', 'sisl.Geometry.tile')
----> 2 help(sisl.Geometry.tile)

NameError: name 'sisl' is not defined

Hi， @zerothi,
I try to calculate the electronic transport properties of a graphene nanojunction with a charge gate using the Geometry.Charge block and I have two questions about the calculation details.

• Should the option SlabDipoleCorrection be chosen? In the Method part of your paper published in PCCP the slab dipole correction was used, however I did not find this option in the fdf file.

• If I put a charge -e in the gate plane, how to induce a charge +e in the graphene nanojunction to keep the whole system (the graphene nanojunction + gate) neutral?

Thanks for your kind help.
 
Regards,
Haoyang

I was trying to do two nanotubes, one in the other, in magnetic field. However, when I try to do tbtrans calculations, I get an error: Erroneous electrode setup, check out-put. My code:
import math
import sisl
import numpy as np
import matplotlib.pyplot as plt
from tqdm import tqdm
from functools import partial
%matplotlib inline
elec_in = sisl.geom.nanotube(1, atoms=sisl.Atom(6, R=5+0.01), chirality=(6, 6))
nano_in = elec_in.tile(10, 2)
elec_out = sisl.geom.nanotube(1, atoms=sisl.Atom(6, R=5+0.01), chirality=(11, 11))
nano_out = elec_out.tile(10, 2)
elec_out = elec_out.translate([(elec_in.xyz[:, 0].max()-elec_out.xyz[:, 0].max())/2, 0, 0])
elec_out = elec_out.translate([0, (elec_in.xyz[:, 1].max()-elec_out.xyz[:, 1].max())/2, 0])
elec_out = elec_out.translate([0, 0, -elec_in.xyz[:, 2].max()])
elec = elec_in.append(elec_out, 2)
H_elec = sisl.Hamiltonian(elec)
H_elec.construct([[0.1, 1.43], [0., -2.7]])
H_elec.write('ELEC.nc')
nano_out = nano_out.translate([(nano_in.xyz[:, 0].max()-nano_out.xyz[:, 0].max())/2, 0, 0])
nano_out = nano_out.translate([0, (nano_in.xyz[:, 1].max()-nano_out.xyz[:, 1].max())/2, 0])
nano_out = nano_out.translate([0, 0, -nano_in.xyz[:, 2].max()])
device = nano_in.append(nano_out, 2)
H = sisl.Hamiltonian(device)
H.construct(([0.1, 1.43], [0., -2.7]))
H.write('DEVICE.nc')
xy = sisl.Hamiltonian(device)
for ia in device:
edges = H.edges(ia)
Rij = device.Rij(ia, edges)
xy[ia, edges] = Rij[:, 0] * (Rij[:, 1] + 2 * device.xyz[ia, 1])
xy.finalize()
rec_phis = np.arange(1, 51, 4)
for i, rec_phi in enumerate(tqdm(rec_phis, unit="M")):
phi = 1 / rec_phi
dH = H * np.exp(1.0j * xy * 0.5 / rec_phi) - H
with sisl.get_sile('M_{}.dH.nc'.format(rec_phi), mode='w') as fh:
fh.write_delta(dH)

Hello,

Dear @zerothi ,

Sorry to bother you with this issue, We installed the tutorial using the installation script and, at the end, we got the following message:

This script assumes you are using Python 2.7

 Will try and run sisl
    import sisl ; print(sisl.geom.graphene())
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/icamps/.local/lib/python2.7/site-packages/sisl/__init__.py", line 90, in <module>
    from . import linalg
  File "/home/icamps/.local/lib/python2.7/site-packages/sisl/linalg/__init__.py", line 30, in <module>
    from .base import *
  File "/home/icamps/.local/lib/python2.7/site-packages/sisl/linalg/base.py", line 5, in <module>
    from numpy import atleast_1d, atleast_2d
  File "/home/icamps/.local/lib/python2.7/site-packages/numpy/__init__.py", line 140, in <module>
    from . import _distributor_init
ImportError: cannot import name _distributor_init
Failed running sisl, please mail the organizer with the error message (unless some of the installations failed)

I did not get any other messages.

Thanks in advance,

Camps

Hello Nick,
In your TS_04 tutorial, you said "Although we have 4 electrodes we will only use two different chemical potentials One for each chain."

In your vertical carbon chain setup in this tutorial, can one apply 0.5 V between y-1 and y-2 electrode, and apply 0.0 V between x-1 and x-2 electrode? So they will have chemical potenial:
x-1 0.0eV
x-2 0.0eV
y-1 0.25eV
y-2 -0.25eV

Is it allowed in TranSIESTA to have individual control over 4 different chemical potentials? I am trying to do so but have ran into various kinds of errors.

Thank you!

Questions for TB_01

Questions for TB_02

• sdata --vector
• add Nils' tutorial