Keep getting errors for NEGF calculation - Leads setting and warning of energy steps |
- Date: 2015/03/30 05:18
- Name: Kuan Zhou
<kzhou003@ucr.edu>
- Hi,
To test the NEGF of openMX, I am calculating Transmission of MoS2. In my calculation, I keep getting error and warning as below.
I have attached input files and output here.
Thanks for any comment.
Also have a comment on the manual:
The manual says you can change the cell unit setting instead of rotating the structure atom setting. And you also need change k grid, n1 n2 n3.
But is it that for NEGF calculation, you will have to rotate the atoms? In this way, what is the meaning to save the time in the .hks calculation. You still need rotate it later. Maybe I was confused by the manual.
Regards,
KZ
*************************************
Input file fraction for Lead .hks calculation:
Atoms.Number 6
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 S 1.605845353 0.000000000 1.871405846 3.0 3.0
2 Mo 3.210443471 1.620681382 0.935701903 7.0 7.0
3 S 4.815041827 0.000000000 1.871405846 3.0 3.0
4 S 8.026732719 1.620681382 0.935701903 3.0 3.0
5 Mo 9.631340743 0.000000000 1.871405846 7.0 7.0
6 S 11.235898807 1.620681382 0.935701903 3.0 3.0
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
12.8375 0.000 0.000
0.0000 3.1780 0.0000
0.0000 -1.5890 2.7522
Atoms.UnitVectors>
**************************************
Input file fraction for NEGF calculation:
NEGF.filename.hks.l lead-chain.hks
NEGF.filename.hks.r lead-chain.hks
NEGF.Num.Poles 150 # default=150
NEGF.scf.Kgrid 12 12 # default=1 1
NEGF.SCF.Iter.Band 10
NEGF.bias.voltage 0.0 # 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 on # on|off, default=off
NEGF.Dos.energyrange -3.0 2.0 5.0e-3 #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div 200 # default=200
NEGF.Dos.Kgrid 12 12 # default=1 1
NEGF.tran.energydiv 200 # default=200
NEGF.tran.energyrange -3 2 1.0e-3 # default=-10.0 10.0 1.0e-3 (eV)
NEGF.tran.Kgrid 12 12 # default= 1 1
#
# Definition of Atomic Species
#
Species.Number 2
<Definition.of.Atomic.Species
Mo Mo11.0-s2p2d1 Mo_PBE13
S S9.0-s2p2d1 S_PBE13
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
Atoms.Number 6
<Atoms.SpeciesAndCoordinates
1 S 14.443345446 0.000000000 1.871405846 3.0 3.0
2 Mo 16.0479308126 1.620681382 0.935701903 7.0 7.0
3 S 17.65252900 0.000000000 1.871405846 3.0 3.0
4 S 20.86421989458 1.620681382 0.935701903 3.0 3.0
5 Mo 22.46882818258 0.000000000 1.871405846 7.0 7.0
6 S 24.07338598258 1.620681382 0.935701903 3.0 3.0
Atoms.SpeciesAndCoordinates>
#
# Lead-Left
#
LeftLeadAtoms.Number 6
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 S 1.605845353 0.000000000 1.871405846 3.0 3.0
2 Mo 3.210443471 1.620681382 0.935701903 7.0 7.0
3 S 4.815041827 0.000000000 1.871405846 3.0 3.0
4 S 8.026732719 1.620681382 0.935701903 3.0 3.0
5 Mo 9.631340743 0.000000000 1.871405846 7.0 7.0
6 S 11.235898807 1.620681382 0.935701903 3.0 3.0
LeftLeadAtoms.SpeciesAndCoordinates>
#
# Lead-Right
#
RightLeadAtoms.Number 6
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 S 27.280845446 0.000000000 1.871405846 3.0 3.0
2 Mo 28.885443637 1.620681382 0.935701903 7.0 7.0
3 S 30.490041827 0.000000000 1.871405846 3.0 3.0
4 S 33.701732719 1.620681382 0.935701903 3.0 3.0
5 Mo 35.306341007 0.000000000 1.871405846 7.0 7.0
6 S 36.910898807 1.620681382 0.935701903 3.0 3.0
RightLeadAtoms.SpeciesAndCoordinates>
*********************************
error I got from NEGF calculation:
<TRAN_RestartFile called, mode=read pos=left>
<TRAN_Input_HKS>
<TRAN_RestartFile called, mode=read pos=right>
<TRAN_Input_HKS>
Intrinsic chemical potential (eV) of the leads
Left lead: -5.698341214153
Right lead: -5.698341214153
add voltage = 0.0000 (eV) to the left lead: new ChemP (eV): -5.6983
add voltage = 0.0000 (eV) to the right lead: new ChemP (eV): -5.6983
Parameters for the integration of the non-equilibrium part
lower bound: -5.698341214153 (eV)
upper bound: -5.698341214153 (eV)
energy step: 0.020000000000 (eV)
number of steps: 0
Warning: the energy step you specified is larger than the integration range.
<Input_std> L_AN= 1 T_AN= 1 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> L_AN= 2 T_AN= 2 WhatSpecies= 0 USpin= 7.0000 DSpin= 7.0000
<Input_std> L_AN= 3 T_AN= 3 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> L_AN= 4 T_AN= 4 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> L_AN= 5 T_AN= 5 WhatSpecies= 0 USpin= 7.0000 DSpin= 7.0000
<Input_std> L_AN= 6 T_AN= 6 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> ct_AN= 7 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> ct_AN= 8 WhatSpecies= 0 USpin= 7.0000 DSpin= 7.0000
<Input_std> ct_AN= 9 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> ct_AN=10 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> ct_AN=11 WhatSpecies= 0 USpin= 7.0000 DSpin= 7.0000
<Input_std> ct_AN=12 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> R_AN= 1 T_AN=13 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> R_AN= 2 T_AN=14 WhatSpecies= 0 USpin= 7.0000 DSpin= 7.0000
<Input_std> R_AN= 3 T_AN=15 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> R_AN= 4 T_AN=16 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
<Input_std> R_AN= 5 T_AN=17 WhatSpecies= 0 USpin= 7.0000 DSpin= 7.0000
<Input_std> R_AN= 6 T_AN=18 WhatSpecies= 1 USpin= 3.0000 DSpin= 3.0000
The RIGHT lead cannot be superposed on the original cell even after the translation.
Check your atomic coordinates of the RIGHT lead.
TACC: MPI job exited with code: 1
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Re: Keep getting errors for NEGF calculation - Leads setting and warning of energy steps