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Problems with Transport Calculation
Date: 2012/03/10 22:36
Name: Tamal Goswami

Dear Dr. Ozaki,

I was trying to do transport calculation of a system with gold lead. Band calculation to produce .hks files are done with gold crystal structure (one gold atom coordinate and crystal unit vectors). After the calculation with both the leads when I tried to run the so called "central region"(few gold atom coordinates, other than that used in the calculation for lead, are also included), the calculation ends with the error lines given below:

"Invalid values for the initial densities of atom 1
Invalid values for the initial densities of atom 16".

My system includes 14 atoms in the central region and one atom each for two electrodes. The program does not produce any error regarding those gold atoms which are in the central region. Please help me to get out of the problem.

Eagerly waiting for your reply.

Sincerely,

Tamal Goswami
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Re: Problems with Transport Calculation ( No.1 )
Date: 2012/03/23 08:39
Name: T. Ozaki

Hi,

The message just implies that the initial occupation for atoms in the left and
right leads is improper.

Regards,

TO
メンテ
Re: Problems with Transport Calculation ( No.2 )
Date: 2012/03/23 16:43
Name: Tamal Goswami

Dear Dr. Ozaki,
Thank you for your reply. I gave initial spin moments to the gold atoms of lead the same as that I have given in the central molecule section that is 9.5 and 9.5 (as the Au_PBE.vps include 19 electrons as valence electrons). The same 9.5 9.5 initial spin was also used in the central molecule section. Still openmx3.5 returns the same error. Thank you again in advance for your kind reply.

Sincerely Yours,
Tamal Goswami
メンテ
Re: Problems with Transport Calculation ( No.3 )
Date: 2012/03/23 22:56
Name: T. Ozaki

Hi,

Did you use the same pseudopotential and basis functions for
the calculations for leads and NEGF? Please make sure that
Au_PBE.vps (Ver.2006) and Au_PBE11.vps(Ver.2011) contain
different number of valence electrons. Also, the version
of pseudopotential and basis function should be the same
each other.

If you don't mind, could you show us your input files for
both the lead and NEGF calculations?

Regards,

TO
メンテ
Re: Problems with Transport Calculation ( No.4 )
Date: 2012/03/27 20:18
Name: Tamal Goswami

Dear Dr. Ozaki,

Thanks again for your kind cooperation. I am giving the input files for the leads and the NEGF input here. Please help me sorting out the flaws for a smoother application of openmx. One thing more, if you kindly tell me the ways for a faster calculation (if there is any parameter that controls the computation speed or any tricks etc.), it will be very helpful to me in my 64-bit HP xw-4600 Workstation with intel core2 duo processor.

Thanks in advance.

The input file for the left lead is --


#
# File Name
#

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

DATA.PATH ../DFT_DATA


#
# Definition of Atomic Species
#

Species.Number 1
<Definition.of.Atomic.Species
Au Au6.0-s2p1d1 Au_CA
Definition.of.Atomic.Species>


NEGF.output_hks true
NEGF.filename.hks lead-l-gold.hks


#
# Atoms
#

Atoms.Number 1
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Au 4.17496760 2.00000553 4.00001116 9.5 9.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
4.0704 0.0000 0.0000
0.0000 4.0704 0.0000
0.0000 0.0000 4.0704
Atoms.UnitVectors>


#
# SCF or Electronic System
#


scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 1000 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 201 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 10.0 # default=1
scf.Init.Mixing.Weight 0.100 # default=0.30
scf.Min.Mixing.Weight 0.01 # default=0.001
scf.Max.Mixing.Weight 0.105 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0-4 # default=1.0e-6 (Hartree)

scf.restart off

#
# 1D FFT
#

1DFFT.NumGridK 900 # default=900
1DFFT.NumGridR 900 # default=900
1DFFT.EnergyCutoff 3600.0 # default=3DFFT.EnergyCutoff*3.0 (Ry)


#
# MD or Geometry Optimization
#

MD.Type Opt # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 18 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 2000 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)

#
# Band dispersion
#

Band.dispersion off # on|off, default=off
<Band.KPath.UnitCell
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Band.KPath.UnitCell>

Band.Nkpath 1
<Band.kpath
601 0.0 0.0 0.0 0.5 0.0 0.0 G X
Band.kpath>


#
# DOS and PDOS
#

Dos.fileout off # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 601 1 1 # default = Kgrid1 Kgrid2 Kgrid3

DosGauss.fileout off
DosGauss.Num.Mesh 4000
DosGauss.Width 0.01

The input file for the right lead is --

#
# File Name
#

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

DATA.PATH ../DFT_DATA


#
# Definition of Atomic Species
#

Species.Number 1
<Definition.of.Atomic.Species
C C4.5-s2p1 C_CA
Definition.of.Atomic.Species>


NEGF.output_hks true
NEGF.filename.hks lead-r-gold.hks


#
# Atoms
#

Atoms.Number 1
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 19.82503240 1.99999447 3.99998884 2.0 2.0
Atoms.SpeciesAndCoordinates>
<Atoms.UnitVectors
4.0704 0.0000 0.0000
0.0000 4.0704 0.0000
0.0000 0.0000 4.0704
Atoms.UnitVectors>


#
# SCF or Electronic System
#


scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 1000 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 201 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 10.0 # default=1
scf.Init.Mixing.Weight 0.100 # default=0.30
scf.Min.Mixing.Weight 0.01 # default=0.001
scf.Max.Mixing.Weight 0.105 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-4 # default=1.0e-6 (Hartree)

scf.restart off

#
# 1D FFT
#

1DFFT.NumGridK 900 # default=900
1DFFT.NumGridR 900 # default=900
1DFFT.EnergyCutoff 3600.0 # default=3DFFT.EnergyCutoff*3.0 (Ry)


#
# MD or Geometry Optimization
#

MD.Type Opt # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 18 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 2000 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)


#
# Band dispersion
#

Band.dispersion off # on|off, default=off
<Band.KPath.UnitCell
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Band.KPath.UnitCell>

Band.Nkpath 1
<Band.kpath
601 0.0 0.0 0.0 0.5 0.0 0.0 G X
Band.kpath>


#
# DOS and PDOS
#

Dos.fileout off # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 601 1 1 # default = Kgrid1 Kgrid2 Kgrid3

DosGauss.fileout off
DosGauss.Num.Mesh 4000
DosGauss.Width 0.01

The input file for the NEGF calculation is --

#
# File Name
#

System.CurrrentDirectory ./ # default=./
System.Name negf-gold1.5
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)

DATA.PATH ../DFT_DATA



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

NEGF.Num.Poles 100 # defalut=150
NEGF.scf.Kgrid 1 1 # defalut=1 1

NEGF.bias.voltage +1.5 # 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 -20.0 20.0 1.0e-4 #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div 4000 # default=200
NEGF.Dos.Kgrid 1 1 # default=1 1

NEGF.tran.energydiv 800 # default=200
NEGF.tran.energyrange -4 4 0.001 # default=-10.0 10.0 5.0e-3 (eV)
NEGF.tran.Kgrid 1 1 # default= 1 1

#
# Definition of Atomic Species
#

Species.Number 4
<Definition.of.Atomic.Species
C C4.5-s2p1 C_CA
H H5.5-s2 H_CA
Au Au6.0-s2p1d1 Au_CA
Co Co5.5-s1p1d1 Co_CA
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU


Atoms.Number 14
<Atoms.SpeciesAndCoordinates
1 Au 8.17496760 2.00000553 4.00001116 9.5 9.5
2 Co 10.67496760 2.00000553 4.00001116 9.0 6.0
3 Co 17.32503240 1.99999447 3.99998884 9.0 6.0
4 C 12.60496760 2.00000265 4.00001116 2.0 2.0
5 C 13.30248777 1.14323057 3.14802602 2.0 2.0
6 C 13.30247449 2.85658656 4.85165444 2.0 2.0
7 C 14.69719968 1.14262910 3.14823482 2.0 2.0
8 H 12.75229371 0.46748946 2.47727851 0.5 0.5
9 C 14.69761237 2.85681002 4.85127924 2.0 2.0
10 H 12.75287822 3.53204854 5.52308877 0.5 0.5
11 C 15.39503240 1.99993346 3.99986578 2.0 2.0
12 H 15.24706154 0.46689339 2.47716873 0.5 0.5
13 H 15.24729838 3.53259071 5.52257647 0.5 0.5
14 Au 19.82503240 1.99999447 3.99998884 9.5 9.5
Atoms.SpeciesAndCoordinates>

#
# Lead-Left
#


LeftLeadAtoms.Number 1

<Atoms.SpeciesAndCoordinates
1 Au 4.17496760 2.00000553 4.00001116 9.5 9.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
-4.0704 0.0000 0.0000
0.0000 4.0704 0.0000
0.0000 0.0000 4.0704
Atoms.UnitVectors>

#
# Lead-Right
#


RightLeadAtoms.Number 1

<Atoms.SpeciesAndCoordinates
1 Au 23.82503240 1.99999447 3.99998884 9.5 9.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
4.0704 0.0000 0.0000
0.0000 4.0704 0.0000
0.0000 0.0000 4.0704
Atoms.UnitVectors>

#
# SCF or Electronic System
#


scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 2000 # default=40
scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band|NEGF
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 201 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 40.0 # default=1
scf.Init.Mixing.Weight 0.1 # default=0.30
scf.Min.Mixing.Weight 0.04 # default=0.001
scf.Max.Mixing.Weight 0.4 # default=0.40
scf.Mixing.History 60 # default=5
scf.Mixing.StartPulay 20 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-2 # default=1.0e-6 (Hartree)
scf.system.charge 0.0 # default=0.0
scf.restart off

#
# 1D FFT
#

1DFFT.NumGridK 900 # default=900
1DFFT.NumGridR 900 # default=900
1DFFT.EnergyCutoff 3600.0 # default=3DFFT.EnergyCutoff*3.0 (Ry)


#
# MD or Geometry Optimization
#

MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 10 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 200 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)

メンテ
Re: Problems with Transport Calculation ( No.5 )
Date: 2012/03/27 23:12
Name: T.Ozaki

Hi,

It is easy to see that there are many mistakes in your input files.
You calculated a carbon system for the right lead as

<Atoms.SpeciesAndCoordinates
1 C 19.82503240 1.99999447 3.99998884 2.0 2.0
Atoms.SpeciesAndCoordinates>

however, you specified a right lead consisting of Au in the NEGF calculation.

In addition, for the NEGF calculation,

<Atoms.SpeciesAndCoordinates
1 Au 4.17496760 2.00000553 4.00001116 9.5 9.5
Atoms.SpeciesAndCoordinates>

should be

<LeftLeadAtoms.SpeciesAndCoordinates
1 Au 4.17496760 2.00000553 4.00001116 9.5 9.5
LeftLeadAtoms.SpeciesAndCoordinates>

and

<Atoms.SpeciesAndCoordinates
1 Au 23.82503240 1.99999447 3.99998884 9.5 9.5
Atoms.SpeciesAndCoordinates>

should be

<RightLeadAtoms.SpeciesAndCoordinates
1 Au 23.82503240 1.99999447 3.99998884 9.5 9.5
RightLeadAtoms.SpeciesAndCoordinates>


Those are the reason why you encountered the problem.

Also,

In the calculation for the left lead,
"scf.criterion 1.0-4 # default=1.0e-6 (Hartree)"

should be

"scf.criterion 1.0-4e # default=1.0e-6 (Hartree)"


Regards,

TO
メンテ
Re: Problems with Transport Calculation ( No.6 )
Date: 2012/03/28 22:28
Name: Tamal Goswami

Dear Dr. Ozaki,

Thank you for your kind advice. The right lead I only pasted a wrong file with the same name, with which I was trying to see if there is difficulty with only gold or any other element. Anyway, I shall keep in mind the specifications for the right and left lead atom coordinate specifications. Thank you for your kind cooperation. Hope you will help me further if any other difficulty I face.

One more thing to say that, the 'jx' is not compiling in openmx version 3.6, although other things do compile smoothly.

Sincerely,
Tamal Goswami

メンテ

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