Are you sure that the INPUT file is the same between yours and his?
2014-11-24 10:17 GMT+08:00 joyce79928cc . <[email protected]>:
> Dear:
>
> I want to repeat the result got from Prof. Brandbyge's article
> 'Origin Of Current-Induced Forces In An Atomic Gold Wire: A First
> Principles Study'
> I got the same trend in force but the value of the force is not match with
> the result of this article. (pic attached is my result and article's result)
> what's the problem for my calculation?
> below's are my input.
>
> Elec:
> SystemName Elec-Au
> SystemLabel Elec-Au
>
> # Atomic coordinates
> NumberOfAtoms 018
> AtomicCoordinatesFormat Ang
> %block AtomicCoordinatesAndAtomicSpecies
> 0.00000000 1.77345822 0.00000000 1
> 3.07172169 1.77345822 0.00000000 1
> 6.14344338 1.77345822 0.00000000 1
> 1.53586084 4.43364706 0.00000000 1
> 3.07172169 7.09383590 0.00000000 1
> 4.60758253 4.43364706 0.00000000 1
> 6.14344338 7.09383590 0.00000000 1
> 7.67930422 4.43364706 0.00000000 1
> 9.21516507 7.09383590 0.00000000 1
> -1.53586084 0.88672961 2.50127158 1
> 1.53586084 0.88672961 2.50127158 1
> 4.60758253 0.88672961 2.50127158 1
> 0.00000000 3.54691845 2.50127158 1
> 1.53586084 6.20710728 2.50127158 1
> 3.07172169 3.54691845 2.50127158 1
> 4.60758253 6.20710728 2.50127158 1
> 6.14344338 3.54691845 2.50127158 1
> 7.67930422 6.20710728 2.50127158 1
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> # UNIT CELL
> LatticeConstant 1.0 Ang
> %block LatticeVectors
> 9.21529607 0.00000000 0.00000000
> 4.60764854 7.98068051 0.00000000
> 0.00000000 0.00000000 4.99155000
> %endblock LatticeVectors
>
>
> # K-points
>
> %block kgrid_Monkhorst_Pack
> 1 0 0 0.0
> 0 1 0 0.0
> 0 0 10 0.5
> %endblock kgrid_Monkhorst_Pack
>
>
> # Chemical species
>
> NumberOfSpecies 1
> %block ChemicalSpeciesLabel
> 1 79 Au
> %endblock ChemicalSpeciesLabel
>
> # Basis set variables
> PAO.BasisType split
> PAO.BasisSize SZP
> PAO.energyshift 0.005 Ry
> PAO.BasisType split
>
> # General variables
>
> ElectronicTemperature 300 K
> SolutionMethod diagon
> MeshCutoff 200. Ry
> xc.functional LDA # Exchange-correlation functional
> xc.authors CA
> SpinPolarized false
> # Exchange-correlation version
>
> # SCF variables
>
> DM.MixSCF1 T
> MaxSCFIterations 100 # Maximum number of SCF iter
> DM.MixH T
> DM.MixingWeight 0.03 # New DM amount for next SCF cycle
> DM.Tolerance 1.d-4 # Tolerance in maximum difference
> DM.UseSaveDM true # to use continuation files
> DM.NumberPulay 6
> OccupationFunction MP
>
> # MD variables
>
> MD.FinalTimeStep 1
> MD.TypeOfRun CG
> MD.NumCGsteps 000
> MD.UseSaveXV .true.
>
> # Output variables
>
> WriteMullikenPop 1
> WriteBands .false.
> SaveRho .false.
> SaveDeltaRho .false.
> SaveHS .false.
> SaveElectrostaticPotential no
> SaveTotalPotential no
> WriteCoorXmol .true.
> WriteMDXmol .true.
> WriteMDhistory .false.
> WriteEigenvalues yes
>
> scatter:
> SystemName BDT-Au-1K
> SystemLabel BDT-Au-1K
>
>
> TS.SaveHS .true.
> TS.SaveLead .true.
>
> # ATOMIC POSITIONS
> # Atomic coordinates
> NumberOfAtoms 84
> AtomicCoordinatesFormat Ang
> %block AtomicCoordinatesAndAtomicSpecies
> 0.00000000 0.00000000 0.00000000 1
> 3.07172169 0.00000000 0.00000000 1
> 6.14344338 0.00000000 0.00000000 1
> 1.53586084 2.66018884 0.00000000 1
> 3.07172169 5.32037767 0.00000000 1
> 4.60758253 2.66018884 0.00000000 1
> 6.14344338 5.32037767 0.00000000 1
> 7.67930422 2.66018884 0.00000000 1
> 9.21516507 5.32037767 0.00000000 1
> 0.00000000 1.77345822 2.50127458 1
> 3.07172169 1.77345822 2.50127458 1
> 6.14344338 1.77345822 2.50127458 1
> 1.53586084 4.43364706 2.50127458 1
> 3.07172169 7.09383590 2.50127458 1
> 4.60758253 4.43364706 2.50127458 1
> 6.14344338 7.09383590 2.50127458 1
> 7.67930422 4.43364706 2.50127458 1
> 9.21516507 7.09383590 2.50127458 1
> -1.53586084 0.88672961 5.00254615 1
> 1.53586084 0.88672961 5.00254615 1
> 4.60758253 0.88672961 5.00254615 1
> 0.00000000 3.54691845 5.00254615 1
> 1.53586084 6.20710728 5.00254615 1
> 3.07172169 3.54691845 5.00254615 1
> 4.60758253 6.20710728 5.00254615 1
> 6.14344338 3.54691845 5.00254615 1
> 7.67930422 6.20710728 5.00254615 1
> 0.00000100 0.00000000 7.49282457 1
> 3.07172169 0.00000000 7.49282457 1
> 6.14344338 0.00000000 7.49282457 1
> 1.53586084 2.66018884 7.49282557 1
> 3.07172169 5.32037767 7.49282557 1
> 4.60758253 2.66018884 7.49282557 1
> 6.14344238 5.32037767 7.49282557 1
> 7.67930422 2.66018884 7.49282557 1
> 9.21516507 5.32037767 7.49282557 1
> 0.00000000 1.77345822 10.00842135 1
> 3.07172169 1.77345822 10.00842135 1
> 6.14344338 1.77345822 10.00842135 1
> 1.53586184 4.43364706 10.00842135 1
> 3.07172269 7.09383590 10.00842135 1
> 4.60758353 4.43364706 10.00842135 1
> 6.14344438 7.09383590 10.00842135 1
> 7.67930522 4.43364706 10.00842135 1
> 9.21516507 7.09383590 10.00842135 1
> 3.07172234 3.54691955 12.42011351 1
> 3.07172280 3.54691895 15.36850129 1
> 3.07172241 3.54691961 18.31689056 1
> 0.00000000 1.77345822 20.72857382 1
> 3.07172169 1.77345822 20.72857382 1
> 6.14344338 1.77345822 20.72857382 1
> 1.53586184 4.43364706 20.72857382 1
> 3.07172269 7.09383590 20.72857382 1
> 4.60758353 4.43364706 20.72857382 1
> 6.14344438 7.09383590 20.72857382 1
> 7.67930522 4.43364706 20.72857382 1
> 9.21516507 7.09383590 20.72857382 1
> 0.00000100 0.00000000 23.24416960 1
> 3.07172169 0.00000000 23.24416960 1
> 6.14344338 0.00000000 23.24416960 1
> 1.53586084 2.66018884 23.24416960 1
> 3.07172169 5.32037767 23.24416960 1
> 4.60758253 2.66018884 23.24416960 1
> 6.14344238 5.32037767 23.24416960 1
> 7.67930422 2.66018884 23.24416960 1
> 9.21516507 5.32037767 23.24416960 1
> -1.53586084 0.88672961 25.73444802 1
> 1.53586084 0.88672961 25.73444802 1
> 4.60758253 0.88672961 25.73444802 1
> 0.00000000 3.54691845 25.73444802 1
> 1.53586084 6.20710728 25.73444802 1
> 3.07172169 3.54691845 25.73444802 1
> 4.60758253 6.20710728 25.73444802 1
> 6.14344338 3.54691845 25.73444802 1
> 7.67930422 6.20710728 25.73444802 1
> 0.00000000 1.77345822 28.23571960 1
> 3.07172169 1.77345822 28.23571960 1
> 6.14344338 1.77345822 28.23571960 1
> 1.53586084 4.43364706 28.23571960 1
> 3.07172169 7.09383590 28.23571960 1
> 4.60758253 4.43364706 28.23571960 1
> 6.14344338 7.09383590 28.23571960 1
> 7.67930422 4.43364706 28.23571960 1
> 9.21516507 7.09383590 28.23571960 1
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> # UNIT CELL
> LatticeConstant 1.0 Ang
> %block LatticeVectors
> 9.21529607 0.00000000 0.00000000
> 4.60764854 7.98068051 0.00000000
> 0.00000000 0.00000000 30.73699118
> %endblock LatticeVectors
>
>
> # K-points
>
> %block kgrid_Monkhorst_Pack
> 4 0 0 0.0
> 0 4 0 0.0
> 0 0 4 0.0
> %endblock kgrid_Monkhorst_Pack
>
>
> # Chemical species
>
> NumberOfSpecies 1
> %block ChemicalSpeciesLabel
> 1 79 Au
> %endblock ChemicalSpeciesLabel
>
> # Basis set variables
>
> PAO.BasisType split
> PAO.BasisSize SZP
> PAO.BasisType split # Type of basis ('nones',
> 'nonodes', 'split')
> PAO.energyshift 0.005 Ry
>
> # General variables
>
> ElectronicTemperature 300 K
>
> SolutionMethod transiesta
> MeshCutoff 200. Ry
> xc.functional LDA # Exchange-correlation functional
> xc.authors CA
> SpinPolarized false
> # Exchange-correlation version
>
> # SCF variables
>
> DM.MixSCF1 T
> MaxSCFIterations 100 # Maximum number of SCF iter
> DM.MixH T
> DM.MixingWeight 0.03 # New DM amount for next SCF cycle
> DM.Tolerance 1.d-4 # Tolerance in maximum difference
> DM.UseSaveDM true # to use continuation files
> DM.NumberPulay 5
> OccupationFunction MP
>
> # MD variables
>
> MD.FinalTimeStep 1
> MD.TypeOfRun CG
> MD.NumCGsteps 000
> #%block GeometryConstraints
> #position from 1 to 36
> #position from 41 to 85
> #%endblock GeometryConstraints
> MD.UseSaveXV .true.
> UseSaveData .true.
>
> # Output variables
>
> WriteMullikenPop 1
> WriteBands .false.
> SaveRho .false.
> SaveDeltaRho .false.
> SaveHS .true.
> SaveElectrostaticPotential no
> SaveTotalPotential no
> WriteCoorXmol .true.
> WriteMDXmol .true.
> WriteMDhistory .false.
> WriteEigenvalues yes
>
> TS.Voltage 2.0 eV
> TS.biasContour.NumPoints 100
> TS.biasContour.Eta 0.001 eV
> SaveTotalPotential T
> SaveRho T
> SaveElectrostaticPotential T
>
> #------------------------------------
> # ELECTRODES
> # -----------------------------------
> # LEFT ELECTRODE
> TS.HSFileLeft '../../elec/4x4/Elec-Au.TSHS'
> TS.NumUsedAtomsLeft 18
> TS.BufferAtomsLeft 9
> # RIGHT ELECTRODE
> TS.HSFileRight '../../elecCBA/4x4/Elec-Au.TSHS'
> TS.NumUsedAtomsRight 18
>
> can somebody help with my problem?
> Thanks a lot!
>
> --
> Best Regards
>
> 邱芳瑜 Chiu Fang Yu
> 國立成功大學 材料科學與工程學系碩二
> MOBILE：0930287221(中華)
> GMAIL：[email protected] <[email protected]>
>
>
>
> 2014-11-16 19:34 GMT+08:00 joyce79928cc . <[email protected]>:
>
> Dear:
>>
>> I want to repeat the result got from Prof. Brandbyge's article
>> 'Origin Of Current-Induced Forces In An Atomic Gold Wire: A First
>> Principles Study'
>> I got the same trend in force but the value of the force is not match
>> with the result of this article. (pic attached is my result and article's
>> result)
>> what's the problem for my calculation?
>> below's are my input.
>>
>> Elec:
>> SystemName Elec-Au
>> SystemLabel Elec-Au
>>
>> # Atomic coordinates
>> NumberOfAtoms 018
>> AtomicCoordinatesFormat Ang
>> %block AtomicCoordinatesAndAtomicSpecies
>> 0.00000000 1.77345822 0.00000000 1
>> 3.07172169 1.77345822 0.00000000 1
>> 6.14344338 1.77345822 0.00000000 1
>> 1.53586084 4.43364706 0.00000000 1
>> 3.07172169 7.09383590 0.00000000 1
>> 4.60758253 4.43364706 0.00000000 1
>> 6.14344338 7.09383590 0.00000000 1
>> 7.67930422 4.43364706 0.00000000 1
>> 9.21516507 7.09383590 0.00000000 1
>> -1.53586084 0.88672961 2.50127158 1
>> 1.53586084 0.88672961 2.50127158 1
>> 4.60758253 0.88672961 2.50127158 1
>> 0.00000000 3.54691845 2.50127158 1
>> 1.53586084 6.20710728 2.50127158 1
>> 3.07172169 3.54691845 2.50127158 1
>> 4.60758253 6.20710728 2.50127158 1
>> 6.14344338 3.54691845 2.50127158 1
>> 7.67930422 6.20710728 2.50127158 1
>> %endblock AtomicCoordinatesAndAtomicSpecies
>>
>> # UNIT CELL
>> LatticeConstant 1.0 Ang
>> %block LatticeVectors
>> 9.21529607 0.00000000 0.00000000
>> 4.60764854 7.98068051 0.00000000
>> 0.00000000 0.00000000 4.99155000
>> %endblock LatticeVectors
>>
>>
>> # K-points
>>
>> %block kgrid_Monkhorst_Pack
>> 1 0 0 0.0
>> 0 1 0 0.0
>> 0 0 10 0.5
>> %endblock kgrid_Monkhorst_Pack
>>
>>
>> # Chemical species
>>
>> NumberOfSpecies 1
>> %block ChemicalSpeciesLabel
>> 1 79 Au
>> %endblock ChemicalSpeciesLabel
>>
>> # Basis set variables
>> PAO.BasisType split
>> PAO.BasisSize SZP
>> PAO.energyshift 0.005 Ry
>> PAO.BasisType split
>>
>> # General variables
>>
>> ElectronicTemperature 300 K
>> SolutionMethod diagon
>> MeshCutoff 200. Ry
>> xc.functional LDA # Exchange-correlation functional
>> xc.authors CA
>> SpinPolarized false
>> # Exchange-correlation version
>>
>> # SCF variables
>>
>> DM.MixSCF1 T
>> MaxSCFIterations 100 # Maximum number of SCF iter
>> DM.MixH T
>> DM.MixingWeight 0.03 # New DM amount for next SCF cycle
>> DM.Tolerance 1.d-4 # Tolerance in maximum difference
>> DM.UseSaveDM true # to use continuation files
>> DM.NumberPulay 6
>> OccupationFunction MP
>>
>> # MD variables
>>
>> MD.FinalTimeStep 1
>> MD.TypeOfRun CG
>> MD.NumCGsteps 000
>> MD.UseSaveXV .true.
>>
>> # Output variables
>>
>> WriteMullikenPop 1
>> WriteBands .false.
>> SaveRho .false.
>> SaveDeltaRho .false.
>> SaveHS .false.
>> SaveElectrostaticPotential no
>> SaveTotalPotential no
>> WriteCoorXmol .true.
>> WriteMDXmol .true.
>> WriteMDhistory .false.
>> WriteEigenvalues yes
>>
>> scatter:
>> SystemName BDT-Au-1K
>> SystemLabel BDT-Au-1K
>>
>>
>> TS.SaveHS .true.
>> TS.SaveLead .true.
>>
>> # ATOMIC POSITIONS
>> # Atomic coordinates
>> NumberOfAtoms 84
>> AtomicCoordinatesFormat Ang
>> %block AtomicCoordinatesAndAtomicSpecies
>> 0.00000000 0.00000000 0.00000000 1
>> 3.07172169 0.00000000 0.00000000 1
>> 6.14344338 0.00000000 0.00000000 1
>> 1.53586084 2.66018884 0.00000000 1
>> 3.07172169 5.32037767 0.00000000 1
>> 4.60758253 2.66018884 0.00000000 1
>> 6.14344338 5.32037767 0.00000000 1
>> 7.67930422 2.66018884 0.00000000 1
>> 9.21516507 5.32037767 0.00000000 1
>> 0.00000000 1.77345822 2.50127458 1
>> 3.07172169 1.77345822 2.50127458 1
>> 6.14344338 1.77345822 2.50127458 1
>> 1.53586084 4.43364706 2.50127458 1
>> 3.07172169 7.09383590 2.50127458 1
>> 4.60758253 4.43364706 2.50127458 1
>> 6.14344338 7.09383590 2.50127458 1
>> 7.67930422 4.43364706 2.50127458 1
>> 9.21516507 7.09383590 2.50127458 1
>> -1.53586084 0.88672961 5.00254615 1
>> 1.53586084 0.88672961 5.00254615 1
>> 4.60758253 0.88672961 5.00254615 1
>> 0.00000000 3.54691845 5.00254615 1
>> 1.53586084 6.20710728 5.00254615 1
>> 3.07172169 3.54691845 5.00254615 1
>> 4.60758253 6.20710728 5.00254615 1
>> 6.14344338 3.54691845 5.00254615 1
>> 7.67930422 6.20710728 5.00254615 1
>> 0.00000100 0.00000000 7.49282457 1
>> 3.07172169 0.00000000 7.49282457 1
>> 6.14344338 0.00000000 7.49282457 1
>> 1.53586084 2.66018884 7.49282557 1
>> 3.07172169 5.32037767 7.49282557 1
>> 4.60758253 2.66018884 7.49282557 1
>> 6.14344238 5.32037767 7.49282557 1
>> 7.67930422 2.66018884 7.49282557 1
>> 9.21516507 5.32037767 7.49282557 1
>> 0.00000000 1.77345822 10.00842135 1
>> 3.07172169 1.77345822 10.00842135 1
>> 6.14344338 1.77345822 10.00842135 1
>> 1.53586184 4.43364706 10.00842135 1
>> 3.07172269 7.09383590 10.00842135 1
>> 4.60758353 4.43364706 10.00842135 1
>> 6.14344438 7.09383590 10.00842135 1
>> 7.67930522 4.43364706 10.00842135 1
>> 9.21516507 7.09383590 10.00842135 1
>> 3.07172234 3.54691955 12.42011351 1
>> 3.07172280 3.54691895 15.36850129 1
>> 3.07172241 3.54691961 18.31689056 1
>> 0.00000000 1.77345822 20.72857382 1
>> 3.07172169 1.77345822 20.72857382 1
>> 6.14344338 1.77345822 20.72857382 1
>> 1.53586184 4.43364706 20.72857382 1
>> 3.07172269 7.09383590 20.72857382 1
>> 4.60758353 4.43364706 20.72857382 1
>> 6.14344438 7.09383590 20.72857382 1
>> 7.67930522 4.43364706 20.72857382 1
>> 9.21516507 7.09383590 20.72857382 1
>> 0.00000100 0.00000000 23.24416960 1
>> 3.07172169 0.00000000 23.24416960 1
>> 6.14344338 0.00000000 23.24416960 1
>> 1.53586084 2.66018884 23.24416960 1
>> 3.07172169 5.32037767 23.24416960 1
>> 4.60758253 2.66018884 23.24416960 1
>> 6.14344238 5.32037767 23.24416960 1
>> 7.67930422 2.66018884 23.24416960 1
>> 9.21516507 5.32037767 23.24416960 1
>> -1.53586084 0.88672961 25.73444802 1
>> 1.53586084 0.88672961 25.73444802 1
>> 4.60758253 0.88672961 25.73444802 1
>> 0.00000000 3.54691845 25.73444802 1
>> 1.53586084 6.20710728 25.73444802 1
>> 3.07172169 3.54691845 25.73444802 1
>> 4.60758253 6.20710728 25.73444802 1
>> 6.14344338 3.54691845 25.73444802 1
>> 7.67930422 6.20710728 25.73444802 1
>> 0.00000000 1.77345822 28.23571960 1
>> 3.07172169 1.77345822 28.23571960 1
>> 6.14344338 1.77345822 28.23571960 1
>> 1.53586084 4.43364706 28.23571960 1
>> 3.07172169 7.09383590 28.23571960 1
>> 4.60758253 4.43364706 28.23571960 1
>> 6.14344338 7.09383590 28.23571960 1
>> 7.67930422 4.43364706 28.23571960 1
>> 9.21516507 7.09383590 28.23571960 1
>> %endblock AtomicCoordinatesAndAtomicSpecies
>>
>> # UNIT CELL
>> LatticeConstant 1.0 Ang
>> %block LatticeVectors
>> 9.21529607 0.00000000 0.00000000
>> 4.60764854 7.98068051 0.00000000
>> 0.00000000 0.00000000 30.73699118
>> %endblock LatticeVectors
>>
>>
>> # K-points
>>
>> %block kgrid_Monkhorst_Pack
>> 4 0 0 0.0
>> 0 4 0 0.0
>> 0 0 4 0.0
>> %endblock kgrid_Monkhorst_Pack
>>
>>
>> # Chemical species
>>
>> NumberOfSpecies 1
>> %block ChemicalSpeciesLabel
>> 1 79 Au
>> %endblock ChemicalSpeciesLabel
>>
>> # Basis set variables
>>
>> PAO.BasisType split
>> PAO.BasisSize SZP
>> PAO.BasisType split # Type of basis ('nones',
>> 'nonodes', 'split')
>> PAO.energyshift 0.005 Ry
>>
>> # General variables
>>
>> ElectronicTemperature 300 K
>>
>> SolutionMethod transiesta
>> MeshCutoff 200. Ry
>> xc.functional LDA # Exchange-correlation functional
>> xc.authors CA
>> SpinPolarized false
>> # Exchange-correlation version
>>
>> # SCF variables
>>
>> DM.MixSCF1 T
>> MaxSCFIterations 100 # Maximum number of SCF iter
>> DM.MixH T
>> DM.MixingWeight 0.03 # New DM amount for next SCF cycle
>> DM.Tolerance 1.d-4 # Tolerance in maximum difference
>> DM.UseSaveDM true # to use continuation files
>> DM.NumberPulay 5
>> OccupationFunction MP
>>
>> # MD variables
>>
>> MD.FinalTimeStep 1
>> MD.TypeOfRun CG
>> MD.NumCGsteps 000
>> #%block GeometryConstraints
>> #position from 1 to 36
>> #position from 41 to 85
>> #%endblock GeometryConstraints
>> MD.UseSaveXV .true.
>> UseSaveData .true.
>>
>> # Output variables
>>
>> WriteMullikenPop 1
>> WriteBands .false.
>> SaveRho .false.
>> SaveDeltaRho .false.
>> SaveHS .true.
>> SaveElectrostaticPotential no
>> SaveTotalPotential no
>> WriteCoorXmol .true.
>> WriteMDXmol .true.
>> WriteMDhistory .false.
>> WriteEigenvalues yes
>>
>> TS.Voltage 2.0 eV
>> TS.biasContour.NumPoints 100
>> TS.biasContour.Eta 0.001 eV
>> SaveTotalPotential T
>> SaveRho T
>> SaveElectrostaticPotential T
>>
>> #------------------------------------
>> # ELECTRODES
>> # -----------------------------------
>> # LEFT ELECTRODE
>> TS.HSFileLeft '../../elec/4x4/Elec-Au.TSHS'
>> TS.NumUsedAtomsLeft 18
>> TS.BufferAtomsLeft 9
>> # RIGHT ELECTRODE
>> TS.HSFileRight '../../elecCBA/4x4/Elec-Au.TSHS'
>> TS.NumUsedAtomsRight 18
>>
>> can somebody help with my problem?
>> Thanks a lot!
>> --
>> Best Regards
>>
>> 邱芳瑜 Chiu Fang Yu
>> 國立成功大學 材料科學與工程學系碩二
>> MOBILE：0930287221(中華)
>> GMAIL：[email protected] <[email protected]>
>>
>>
>>
>
