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guohuazhon

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[求助] transiesta 计算错误

这一阵子试着用transiesta，计算例子的时候没有问题，可用自己的输入文件用transiesta计算时没有问题，当用tbtrans的时候就出现如下问题
ERROR: Unexpected no. orbs. in L elec.
ERROR: lastoL,NGL2 0 60
ERROR: Unexpected no. orbs. in L elec.
ERROR STOP from Node: 0
ERROR STOP from Node: 0
求助，望高手指点。另外，我使用的是siesta 3.0 rc2版本。当然能提供一个电极和散射区的输入例子就更好了。

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1楼 2011-08-21 08:53:25

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zhangguangping

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★ ★ ★
guohuazhon(金币+5): 谢谢！广平兄辛苦了，呵呵！ 2011-08-21 17:07:11
zzy870720z(金币+3): guangping兄太热情了，呵呵，辛苦了 2011-09-01 10:50:07

引用回帖:

1楼: Originally posted by guohuazhon at 2011-08-21 08:53:25:
这一阵子试着用transiesta，计算例子的时候没有问题，可用自己的输入文件用transiesta计算时没有问题，当用tbtrans的时候就出现如下问题
ERROR: Unexpected no. orbs. in L elec.
ERROR: lastoL,NGL2 ...

散射区的输入文件：
SystemName  scatter_region_symm-0.0
SystemLabel scatter_region_symm-0.0

TS.biasContour.NumPoints       15
TS.Voltage  0.0  eV

TS.TBT.PDOSFrom  37
TS.TBT.PDOSTo 74

NumberOfSpecies 1
NumberOfAtoms 110

%block ChemicalSpeciesLabel
  1 79 Au
%endblock ChemicalSpeciesLabel

PAO.EnergyShift    100 meV

PAO.BasisType split

%block PAO.BasisSizes
Au  SZP
%endblock PAO.BasisSizes

LatticeConstant 1.0 Ang

%block LatticeVectors
8.65128000 0.00000000 0.00000000
0.00000000 9.98964000 0.00000000
0.00000000 0.00000000 46.08670000
%endblock LatticeVectors

#kgrid_cutoff 20. Ang

%block kgrid_Monkhorst_Pack
  4 0 0 0.5
  0 4 0 0.5
  0 0 1 0.0
%endblock kgrid_Monkhorst_Pack

# SPIN options

xc.functional       GGA          # Exchange-correlation functional
xc.authors          PBE          # Exchange-correlation version
SpinPolarized       F             # Logical parameters are: yes or no
FixSpin             F
TotalSpin          0.0
NonCollinearSpin    F                # 'T', 'F'
MeshCutoff            300. Ry             # Equivalent plane wave cutoff for the grid

# SCF options

DM.Tolerance       1.d-4       # Tolerance in maximum difference between input and output DM
MaxSCFIterations    300       # Maximum number of SCF iter
DM.UseSaveDM          T          # to use continuation files
DM.MixingWeight    0.01       # New DM amount for next SCF cycle
DM.NumberPulay       5
DM.MixSCF1          F
DM.PulayOnFile    F          # Store in memory ('F') or in files ('T')
# NeglNonOverlapInt    T          # 'F'=do not neglect
SolutionMethod       transiesta       # OrderN or Diagon or transiesta if you do a transport calculation
ElectronicTemperature  300 K       # Temp. for Fermi smearing

# MD options

MD.TypeOfRun          CG          # Type of dynamics:
MD.VariableCell       F
MD.NumCGsteps       000          # Number of CG steps for coordinate optimization
ZM.UnitsLength       Ang          #the units of length used during Z-matrix input
ZM.UnitsAngle       deg          #the units of angles used during Z-matrix input
ZM.ForceTolLength    0.02 eV/Ang #controls the convergence with respect to forces on Z-matrix lengths
ZM.ForceTolAngle    0.00356549 Ry/rad    #controls the convergence with respect to forces on Z-matrix angles
ZM.MaxDisplLength    0.1  Ang    # controls the maximum change in a Zmatrix length during an optimisation step
ZM.MaxDisplAngle    0.003 rad    # controls the maximum change in a Z-matrix angle during an optimisation step
ZM.CalcAllForces    T          # Default value

AtomicCoordinatesFormat Ang

%block AtomicCoordinatesAndAtomicSpecies
2.883760 8.324698 -4.709160    1
5.767520 8.324698 -4.709160    1
0.000000 8.324698 -4.709160    1
4.325640 0.832467 -4.709160    1
7.209400 0.832467 -4.709160    1
1.441880 0.832467 -4.709160    1
2.883760 3.329876 -4.709160    1
5.767520 3.329876 -4.709160    1
0.000000 3.329876 -4.709160    1
4.325640 5.827285 -4.709160    1
7.209400 5.827285 -4.709160    1
1.441880 5.827285 -4.709160    1
4.325640 9.157169 -2.354580    1
7.209400 9.157169 -2.354580    1
1.441880 9.157169 -2.354580    1
5.767520 1.664938 -2.354580    1
0.000000 1.664938 -2.354580    1
2.883760 1.664938 -2.354580    1
4.325640 4.162347 -2.354580    1
7.209400 4.162347 -2.354580    1
1.441880 4.162347 -2.354580    1
5.767520 6.659756 -2.354580    1
0.000000 6.659756 -2.354580    1
2.883760 6.659756 -2.354580    1
5.767520 0.000000 0.000000    1
0.000000 0.000000 0.000000    1
2.883760 0.000000 0.000000    1
7.209400 2.497409 0.000000    1
1.441880 2.497409 0.000000    1
4.325640 2.497409 0.000000    1
5.767520 4.994818 0.000000    1
0.000000 4.994818 0.000000    1
2.883760 4.994818 0.000000    1
7.209400 7.492227 0.000000    1
1.441880 7.492227 0.000000    1
4.325640 7.492227 0.000000    1
2.883760 8.324698 2.354580    1
5.767520 8.324698 2.354580    1
0.000000 8.324698 2.354580    1
4.325640 0.832467 2.354580    1
7.209400 0.832467 2.354580    1
1.441880 0.832467 2.354580    1
2.883760 3.329876 2.354580    1
5.767520 3.329876 2.354580    1
0.000000 3.329876 2.354580    1
4.325640 5.827285 2.354580    1
7.209400 5.827285 2.354580    1
1.441880 5.827285 2.354580    1
4.325640 4.162347 4.709160    1
5.767520 6.659756 4.709160    1
2.883760 6.659756 4.709160    1
4.325640 5.827285 7.063740    1
4.325640 5.827285 9.947500    1
4.325640 5.827285 12.831260    1
4.325640 5.827285 15.715020    1
4.325640 5.827285 18.598780    1
4.325640 5.827285 21.482540    1
4.325640 5.827285 24.366300    1
4.325640 5.827285 27.250060    1
4.325640 4.162347 29.604640    1
2.883760 6.659756 29.604640    1
5.767520 6.659756 29.604640    1
5.767520 0.000000 31.959220    1
0.000000 0.000000 31.959220    1
2.883760 0.000000 31.959220    1
7.209400 2.497409 31.959220    1
1.441880 2.497409 31.959220    1
4.325640 2.497409 31.959220    1
5.767520 4.994818 31.959220    1
0.000000 4.994818 31.959220    1
2.883760 4.994818 31.959220    1
7.209400 7.492227 31.959220    1
1.441880 7.492227 31.959220    1
4.325640 7.492227 31.959220    1
2.883760 8.324698 34.313800    1
5.767520 8.324698 34.313800    1
0.000000 8.324698 34.313800    1
4.325640 0.832467 34.313800    1
7.209400 0.832467 34.313800    1
1.441880 0.832467 34.313800    1
2.883760 3.329876 34.313800    1
5.767520 3.329876 34.313800    1
0.000000 3.329876 34.313800    1
4.325640 5.827285 34.313800    1
7.209400 5.827285 34.313800    1
1.441880 5.827285 34.313800    1
4.325640 9.157169 36.668380    1
7.209400 9.157169 36.668380    1
1.441880 9.157169 36.668380    1
5.767520 1.664938 36.668380    1
0.000000 1.664938 36.668380    1
2.883760 1.664938 36.668380    1
4.325640 4.162347 36.668380    1
7.209400 4.162347 36.668380    1
1.441880 4.162347 36.668380    1
5.767520 6.659756 36.668380    1
0.000000 6.659756 36.668380    1
2.883760 6.659756 36.668380    1
5.767520 0.000000 39.022960    1
0.000000 0.000000 39.022960    1
2.883760 0.000000 39.022960    1
7.209400 2.497409 39.022960    1
1.441880 2.497409 39.022960    1
4.325640 2.497409 39.022960    1
5.767520 4.994818 39.022960    1
0.000000 4.994818 39.022960    1
2.883760 4.994818 39.022960    1
7.209400 7.492227 39.022960    1
1.441880 7.492227 39.022960    1
4.325640 7.492227 39.022960    1
%endblock AtomicCoordinatesAndAtomicSpecies

#WriteWaveFunctions       T          # coefficients of the wavefunctions in the basis set orbitals expansion
#WaveFuncKPointsScale    ReciprocalLatticeVectors
#%block WaveFuncKPoints
#0.000 0.000 0.000  from 1 to 10    # Gamma wavefuncs 1 to 10
#%endblock WaveFuncKPoints

# Output options

WriteCoorInitial       T
WriteCoorStep          T
WriteCoorXmol          T
WriteForces             T
WriteEigenvalues       F          # If .false., it writes them in the file Systemlabel.EIG
WriteMullikenPop       1          # Write Mulliken Population Analysis
#WriteKpoints          T
#WriteKbands             T
#WriteBands             T
WriteMDCoorXmol          T
WriteMDhistory          T

# Options for saving or reading information

MD.UseSaveZM             T    # Use stored positions and velocities
MD.UseSaveCG             T    # Use stored positions and velocities
SaveRho                   T    # Write valence pseudocharge at the mesh
SaveDeltaRho             T    # Write RHOscf-RHOatm at the mesh
SaveElectrostaticPotential  T    # Write the total elect. pot. at the mesh
                              # (local pseudopotential + Hartree)
SaveTotalPotential       T    # write the valence total effective local potential
                              # (local pseudopotential + Hartree + Vxc)
WriteSiestaDim             T    # Write minimum dim to siesta.h and stop
WriteDenchar             T    # Write information for DENCHAR

#######################TRANSIESTA OPTIONS#######################
# GF OPTIONS

TS.ComplexContour.Emin    -50.0 eV
TS.ComplexContour.NPoles       16
TS.ComplexContour.NCircle       16
TS.ComplexContour.NLine       11

# BIAS OPTIONS


TS.UpdateDMCROnly             true

# TS OPTIONS

# TBT OPTIONS
TS.CalcGF  F
TS.MixH T
TS.TBT.Emin                -1.0 eV
TS.TBT.Emax                   1.0 eV
TS.TBT.NPoints             100
TS.TBT.NEigen                10
TS.TBT.Eta                1.d-6 Ry

# Write hamiltonian

TS.SaveHS                   true

# LEFT ELECTRODE
TS.HSFileLeft          ./bulk_electrode.TSHS
TS.ReplicateA1Left    1
TS.ReplicateA2Left    1
TS.NumUsedAtomsLeft    36
TS.BufferAtomsLeft    0

# RIGHT ELECTRODE
TS.HSFileRight          ./bulk_electrode.TSHS
TS.ReplicateA1Right    1
TS.ReplicateA2Right    1
TS.NumUsedAtomsRight    36
TS.BufferAtomsRight    0

#######################TRANSIESTA OPTIONS#######################

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弘德明志博学笃行

4楼2011-08-21 13:56:34

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zhangguangping

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【答案】应助回帖

★
guohuazhon(金币+5): 谢谢，按照提示，问题解决了！ 2011-08-21 17:05:49
zzy870720z(金币+1): 谢谢指教 2011-09-01 10:49:25

引用回帖:

我猜测你在计算tbtrans的时候，输入文件中忘记写出下面两个参数了。虽然手册上有一个默认值，在TranSIESTA的计算中，好像是写不写都无所谓，这个选项不读，而是直接使用的是电极计算中基函数的数目；但是如果在tbtrans中不写，默认值是0，所以出现错误。
TS.NumUsedAtomsLeft
TS.NumUsedAtomsRight

希望这个能解决你的问题。

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2楼2011-08-21 13:50:50

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zhangguangping

木虫 (著名写手)

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专业: 原子和分子物理

【答案】应助回帖

★
guohuazhon(金币+10): 谢谢！ 2011-08-21 17:06:25
zzy870720z(金币+1): 谢谢补充 2011-09-01 10:49:39

引用回帖:

附带上一个套输入文件：
体系结构：

说明：左右电极相同，是一个3*4的Au(111)的ABC结构，三层，每层12个原子。中间是散射区，金连有点长而已。

电极的输入文件：
SystemName  bulk_electrode
SystemLabel bulk_electrode

NumberOfSpecies  1
NumberOfAtoms 36

%block ChemicalSpeciesLabel
1 79  Au
%endblock ChemicalSpeciesLabel

PAO.EnergyShift    100 meV

PAO.BasisType split

PAO.BasisSize SZP

LatticeConstant 1.0 Ang

%block LatticeVectors
8.65128000 0.00000000 0.00000000
0.00000000 9.98964000 0.00000000
0.00000000 0.00000000 7.06374000
%endblock LatticeVectors

#kgrid_cutoff 20. Ang

%block kgrid_Monkhorst_Pack
  4 0 0 0.5
  0 4 0 0.5
  0 0 6 0.5
%endblock kgrid_Monkhorst_Pack

# SPIN options

xc.functional       GGA          # Exchange-correlation functional
xc.authors          PBE          # Exchange-correlation version
SpinPolarized       F             # Logical parameters are: yes or no
FixSpin             F
TotalSpin          0.0
NonCollinearSpin    F                # 'T', 'F'
MeshCutoff            300. Ry             # Equivalent plane wave cutoff for the grid

# SCF options

DM.Tolerance       1.d-4       # Tolerance in maximum difference between input and output DM
MaxSCFIterations    300       # Maximum number of SCF iter
DM.UseSaveDM          T          # to use continuation files
DM.MixingWeight    0.05       # New DM amount for next SCF cycle
DM.NumberPulay       5
DM.MixSCF1          F
DM.PulayOnFile    F          # Store in memory ('F') or in files ('T')
# NeglNonOverlapInt    T          # 'F'=do not neglect
SolutionMethod       Diagon       # OrderN or Diagon or transiesta if you do a transport calculation
ElectronicTemperature  300 K       # Temp. for Fermi smearing

# MD options

MD.TypeOfRun          CG          # Type of dynamics:
MD.VariableCell       F
MD.NumCGsteps       000          # Number of CG steps for coordinate optimization
ZM.UnitsLength       Ang          #the units of length used during Z-matrix input
ZM.UnitsAngle       deg          #the units of angles used during Z-matrix input
ZM.ForceTolLength    0.02 eV/Ang #controls the convergence with respect to forces on Z-matrix lengths
ZM.ForceTolAngle    0.00356549 Ry/rad    #controls the convergence with respect to forces on Z-matrix angles
ZM.MaxDisplLength    0.1  Ang    # controls the maximum change in a Zmatrix length during an optimisation step
ZM.MaxDisplAngle    0.003 rad    # controls the maximum change in a Z-matrix angle during an optimisation step
ZM.CalcAllForces    T          # Default value

AtomicCoordinatesFormat    Ang
%block AtomicCoordinatesAndAtomicSpecies
2.883760 8.324698 -4.709160 1
5.767520 8.324698 -4.709160 1
0.000000 8.324698 -4.709160 1
4.325640 0.832467 -4.709160 1
7.209400 0.832467 -4.709160 1
1.441880 0.832467 -4.709160 1
2.883760 3.329876 -4.709160 1
5.767520 3.329876 -4.709160 1
0.000000 3.329876 -4.709160 1
4.325640 5.827285 -4.709160 1
7.209400 5.827285 -4.709160 1
1.441880 5.827285 -4.709160 1
4.325640 9.157169 -2.354580 1
7.209400 9.157169 -2.354580 1
1.441880 9.157169 -2.354580 1
5.767520 1.664938 -2.354580 1
0.000000 1.664938 -2.354580 1
2.883760 1.664938 -2.354580 1
4.325640 4.162347 -2.354580 1
7.209400 4.162347 -2.354580 1
1.441880 4.162347 -2.354580 1
5.767520 6.659756 -2.354580 1
0.000000 6.659756 -2.354580 1
2.883760 6.659756 -2.354580 1
5.767520 0.000000 0.000000 1
0.000000 0.000000 0.000000 1
2.883760 0.000000 0.000000 1
7.209400 2.497409 0.000000 1
1.441880 2.497409 0.000000 1
4.325640 2.497409 0.000000 1
5.767520 4.994818 0.000000 1
0.000000 4.994818 0.000000 1
2.883760 4.994818 0.000000 1
7.209400 7.492227 0.000000 1
1.441880 7.492227 0.000000 1
4.325640 7.492227 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies

# Output options

WriteCoorInitial       T
WriteCoorStep          T
WriteCoorXmol          T
WriteForces             T
WriteEigenvalues       F          # If .false., it writes them in the file Systemlabel.EIG
WriteMullikenPop       1          # Write Mulliken Population Analysis
#WriteKpoints          T
#WriteKbands             T
#WriteBands             T
WriteMDCoorXmol          T
WriteMDhistory          T

# Options for saving or reading information

MD.UseSaveZM             T    # Use stored positions and velocities
MD.UseSaveCG             T    # Use stored positions and velocities
SaveRho                   T    # Write valence pseudocharge at the mesh
SaveDeltaRho             T    # Write RHOscf-RHOatm at the mesh
SaveElectrostaticPotential  T    # Write the total elect. pot. at the mesh
                              # (local pseudopotential + Hartree)
SaveTotalPotential       T    # write the valence total effective local potential
                              # (local pseudopotential + Hartree + Vxc)
WriteSiestaDim             T    # Write minimum dim to siesta.h and stop
WriteDenchar             T    # Write information for DENCHAR

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弘德明志博学笃行

3楼2011-08-21 13:55:54

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伐木工

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金币: 1989.9
散金: 30
帖子: 33
在线: 56.6小时
虫号: 803034
注册: 2009-07-03
专业: 凝聚态物性 II ：电子结构

引用回帖:

3楼: Originally posted by zhangguangping at 2011-08-21 13:55:54:
附带上一个套输入文件：
体系结构：

说明：左右电极相同，是一个3*4的Au(111)的ABC结构，三层，每层12个原子。中间是散射区，金连有点长而已。

电极的输入文 ...

你好我最近一直在学习transiesta 因为初学所以很想知道对于electrode.fdf和bulk.fdf的原子坐标怎么写，是在写bulk.fdf的原子坐标时还要把电极的坐标也要写在里面吗，请问二楼图中是否含有Au电极，还是不含有电极仅是屏蔽层和散射区原子？非常感谢

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5楼2011-08-31 20:36:34

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