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input files for periodic system under zero bias
Date: 2018/06/29 02:10
Name: Frank

Hi everyone,

I noticed that for the transport calculation, there is a mode namely 'periodic system under zero bias' in the manual. As the manual says, only step1 and step3 are needed. My question is the following:

1. As we know, for the biased calculation, the input file for step1 is for the band calculation of the lead. What about the input file for step1 of the periodic zero bias calculation? Is it still only for the lead? Or it should also include the central scattering region, since step2 is skipped.

2. As the manual says, for step1, a keyword 'NEGF.Output.for.TranMain' should be added. I am wondering if the other keywords should be modified. For example, since step2 is skipped, I think there is no need to generate the .hks file. Am I right?

3. The input file for step3 is used to calculate the transmission, eigenchannel and so on. Are the keywords like 'NEGF.filename.hks.l', 'NEGF.scf.Kgrid', etc.,and atomic coordinates necessary?

I would really appreciate if anyone can provide me examples of the input files for this 'periodic system under zero bias' mode.

Thank you very much.

Best,
Frank
メンテ
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Re: input files for periodic system under zero bias ( No.1 )
Date: 2018/06/29 02:26
Name: Frank

I am sorry I forgot one more question.
Does the keyword 'NEGF.tran.SCF.skip' really work in the version 3.8.5?
It seems it does not work.

Looking forward to your reply.

Thank you very much.

Best,
Frank
メンテ
Re: input files for periodic system under zero bias ( No.2 )
Date: 2018/07/12 01:21
Name: Mitsuaki Kawamura  <mkawamura@issp.u-tokyo.ac.jp>

Dear Frank

Hello,

1, In this case, L0+C+R0 in Fig. 31 of
http://www.openmx-square.org/openmx_man3.8/node114.html
should be specified.

2, *.hks is still needed.

3, NEGF.filename.hks.l(r) is nessesary, but NEGF.scf.Kgrid is not.

4, I found 'NEGF.tran.SCF.skip' works in the version 3.8.5.


I attached the input files for this function.

for step 1

########################################################################
System.CurrrentDirectory ./ # default=./
System.Name lead-chain
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

NEGF.output_hks on
NEGF.filename.hks lead-chain.hks
NEGF.Output.for.TranMain on

#
# Definition of Atomic Species
#

Species.Number 1
<Definition.of.Atomic.Species
C C5.0-s2p2d1 C_CA13
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 9
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C -1.500 0.000 0.000 2.0 2.0
2 C 0.000 0.000 0.000 2.0 2.0
3 C 1.500 0.000 0.000 2.0 2.0
4 C 3.000 0.000 0.000 2.0 2.0
5 C 4.500 0.000 0.000 2.0 2.0
6 C 6.000 0.000 0.000 2.0 2.0
7 C 7.500 0.000 0.000 2.0 2.0
8 C 9.000 0.000 0.000 2.0 2.0
9 C 10.500 0.000 0.000 2.0 2.0
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
13.5 0.0 0.0
0.0 10.0 0.0
0.0 0.0 10.0
Atoms.UnitVectors>

#
# SCF or Electronic System
#

scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 600.0 # default=300 (K)
scf.energycutoff 180.0 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 200 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.010 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.020 # default=0.40
scf.Mixing.History 20 # default=5
scf.Mixing.StartPulay 7 # default=6
scf.criterion 1.0e-10 # default=1.0e-6 (Hartree)
################################################################################

for step 3

################################################################
System.CurrrentDirectory ./ # default=./
System.Name lead-chain
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

NEGF.filename.hks.l lead-chain.hks
NEGF.filename.hks.r lead-chain.hks

NEGF.Num.Poles 100 # default=150
NEGF.scf.Kgrid 1 1 # default=1 1
NEGF.SCF.Iter.Band 50

NEGF.bias.voltage 0.1 # default=0.0 (eV)
NEGF.bias.neq.im.energy 0.01 # default=0.01 (eV)
NEGF.bias.neq.energy.step 0.02 # default=0.02 (eV)

Dos.fileout off # on|off, default=off
NEGF.Dos.energyrange -15.0 25.0 5.0e-3 #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div 200 # default=200
NEGF.Dos.Kgrid 1 1 # default=1 1

#
# Transmission & Eigen Channel
#

NEGF.tran.Analysis on # default on
NEGF.tran.energydiv 200 # default=200
NEGF.tran.energyrange -10 10 1.0e-3 # default=-10.0 10.0 1.0e-3 (eV)
NEGF.tran.Kgrid 1 1 # default= 1 1
NEGF.tran.Channel on # default on
NEGF.Channel.Nkpoint 1 # default=1
<NEGF.Channel.kpoint
0.0 0.0
NEGF.Channel.kpoint>
# default 0.0 0.0
NEGF.Channel.Nenergy 1 # default=1
<NEGF.Channel.energy
0.0
NEGF.Channel.energy>
# default 0.0
NEGF.Channel.Num 5 # defualt=5(for collinear), 10(for Non-collinear)

#
# Definition of Atomic Species
#

Species.Number 1
<Definition.of.Atomic.Species
C C5.0-s2p2d1 C_CA13
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU

Atoms.Number 3
<Atoms.SpeciesAndCoordinates
1 C 3.000 0.000 0.000 2.0 2.0
2 C 4.500 0.000 0.000 2.0 2.0
3 C 6.000 0.000 0.000 2.0 2.0
Atoms.SpeciesAndCoordinates>

#
# Lead-Left
#

LeftLeadAtoms.Number 3
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C -1.500 0.000 0.000 2.0 2.0
2 C 0.000 0.000 0.000 2.0 2.0
3 C 1.500 0.000 0.000 2.0 2.0
LeftLeadAtoms.SpeciesAndCoordinates>

#
# Lead-Right
#

RightLeadAtoms.Number 3
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 7.500 0.000 0.000 2.0 2.0
2 C 9.000 0.000 0.000 2.0 2.0
3 C 10.500 0.000 0.000 2.0 2.0
RightLeadAtoms.SpeciesAndCoordinates>


#
# SCF or Electronic System
#

scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 600.0 # default=300 (K)
scf.energycutoff 180.0 # default=150 (Ry)
scf.maxIter 500 # default=40
scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band
#scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 1 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.020 # default=0.30
scf.Min.Mixing.Weight 0.020 # default=0.001
scf.Max.Mixing.Weight 0.050 # default=0.40
scf.Mixing.History 100 # default=5
scf.Mixing.StartPulay 20 # default=6
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)
scf.Kerker.factor 30.0 # default=1
NEGF.Poisson.Solver FFT
NEGF.tran.SCF.skip on
############################################################

Best regards,
Mitsuaki Kawamura
メンテ
Re: input files for periodic system under zero bias ( No.3 )
Date: 2018/07/15 12:00
Name: Frank

Dear Mitsuaki,

Thanks for your reply.
You have totally solved my problem and gave a very helpful example.

Best regards,
Frank
メンテ

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